From 21650ffec3e553868557cf8ea568c42e6da4215c Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 24 Jan 2023 14:05:39 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9101@7b00b4f --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 518 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 39143 -> 38228 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 55210 -> 52748 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 28305 -> 27617 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 37719 -> 40949 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 37904 -> 38360 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 50479 -> 49105 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 41889 -> 42037 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28459 -> 28485 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78234 -> 78272 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49877 -> 49923 bytes articles/EUCAST.html | 2 +- articles/MDR.html | 60 +- articles/PCA.html | 2 +- articles/SPSS.html | 2 +- articles/WHONET.html | 2 +- articles/datasets.html | 2 +- articles/index.html | 2 +- articles/resistance_predict.html | 2 +- articles/welcome_to_AMR.html | 2 +- authors.html | 2 +- index.html | 2 +- news/index.html | 24 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR-options.html | 2 +- reference/AMR.html | 2 +- reference/Rplot005.png | Bin 12947 -> 12795 bytes reference/Rplot006.png | Bin 12461 -> 12319 bytes reference/Rplot007.png | Bin 14717 -> 15707 bytes reference/Rplot008.png | Bin 18935 -> 18641 bytes reference/Rplot009.png | Bin 8645 -> 8406 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/antibiotic_class_selectors.html | 2 +- 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 | 2 +- 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 | 142 +++-- 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 | 89 ++- 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 26172 -> 26813 bytes reference/plot-2.png | Bin 26436 -> 27523 bytes reference/plot-3.png | Bin 28391 -> 28569 bytes reference/plot-4.png | Bin 38066 -> 38725 bytes reference/plot-5.png | Bin 38045 -> 39021 bytes reference/plot-6.png | Bin 36859 -> 37670 bytes reference/plot-7.png | Bin 38854 -> 41472 bytes reference/plot-8.png | Bin 56812 -> 55431 bytes reference/plot-9.png | Bin 26444 -> 26145 bytes reference/plot.html | 2 +- reference/proportion.html | 2 +- reference/random.html | 34 +- reference/resistance_predict.html | 2 +- reference/skewness.html | 4 +- reference/translate.html | 2 +- search.json | 2 +- 99 files changed, 521 insertions(+), 530 deletions(-) diff --git a/404.html b/404.html index 7e22b706..799af34f 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 1.8.2.9100 + 1.8.2.9101
So only 60.9% is suitable for resistance analysis! We can now filter +
So only 61.9% is suitable for resistance analysis! We can now filter
on it with the filter()
function, also from the
dplyr
package:
@@ -640,11 +640,11 @@ on it with the data_1st <- data %>%
filter_first_isolate()
# Including isolates from ICU.
So we end up with 12,181 isolates for analysis. Now our data looks +
So we end up with 12,380 isolates for analysis. Now our data looks like:
head(data_1st)
1 | -2016-07-10 | -S7 | +2014-12-24 | +I1 | +Hospital C | +B_STPHY_AURS | +S | +S | +I | +S | +M | +Gram-positive | +Staphylococcus | +aureus | +TRUE | +|||
2 | +2011-04-22 | +J2 | +Hospital A | +B_KLBSL_PNMN | +R | +R | +I | +I | +M | +Gram-negative | +Klebsiella | +pneumoniae | +TRUE | +|||||
3 | +2010-08-09 | +T2 | Hospital D | B_STPHY_AURS | I | S | R | -R | +I | F | Gram-positive | Staphylococcus | @@ -695,14 +727,30 @@ like:TRUE | |||||
4 | -2014-02-21 | -R6 | -Hospital C | -B_ESCHR_COLI | +6 | +2010-03-10 | +J7 | +Hospital B | +B_STPHY_AURS | R | I | R | +R | +M | +Gram-positive | +Staphylococcus | +aureus | +TRUE | +
8 | +2014-08-13 | +T6 | +Hospital D | +B_ESCHR_COLI | +R | +R | +R | S | F | Gram-negative | @@ -710,64 +758,16 @@ like:coli | TRUE | ||||||
11 | -2017-08-05 | -Z10 | -Hospital B | -B_STPHY_AURS | -R | -I | -R | -S | -F | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -|||||
15 | -2017-10-24 | -W2 | -Hospital B | -B_STPHY_AURS | -R | -R | -R | -R | -F | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -|||||
16 | -2017-01-01 | -Y9 | +10 | +2017-02-03 | +A10 | Hospital B | B_ESCHR_COLI | +R | I | S | S | -S | -F | -Gram-negative | -Escherichia | -coli | -TRUE | -|
17 | -2011-09-19 | -K10 | -Hospital C | -B_ESCHR_COLI | -R | -S | -R | -R | M | Gram-negative | Escherichia | @@ -807,8 +807,8 @@ readable:|||||||
1 | Escherichia coli | -5,814 | -47.73% | -5,814 | -47.73% | +5,838 | +47.16% | +5,838 | +47.16% | |||||||||
2 | Staphylococcus aureus | -3,254 | -26.71% | -9,068 | -74.44% | +3,300 | +26.66% | +9,138 | +73.81% | |||||||||
3 | Streptococcus pneumoniae | -1,814 | -14.89% | -10,882 | -89.34% | +1,886 | +15.23% | +11,024 | +89.05% | |||||||||
4 | Klebsiella pneumoniae | -1,299 | -10.66% | -12,181 | +1,356 | +10.95% | +12,380 | 100.00% | ||||||||||
2016-07-10 | -S7 | -Hospital D | +2010-03-10 | +J7 | +Hospital B | B_STPHY_AURS | +R | I | -S | R | R | -F | +M | Gram-positive | Staphylococcus | aureus | TRUE | |
2017-10-24 | -W2 | -Hospital B | -B_STPHY_AURS | +2016-03-10 | +N10 | +Hospital D | +B_ESCHR_COLI | R | R | R | R | F | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -||
2011-09-19 | -K10 | -Hospital C | -B_ESCHR_COLI | -R | -S | -R | -R | -M | Gram-negative | Escherichia | coli | TRUE | ||||||
2016-11-01 | -X5 | -Hospital B | -B_STRPT_PNMN | -S | -S | -R | -R | -F | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -||||||
2015-10-12 | -Q10 | -Hospital B | +2013-06-19 | +X3 | +Hospital A | B_KLBSL_PNMN | R | R | @@ -983,13 +953,43 @@ antibiotic class they are in:TRUE | |||||||||
2016-06-03 | -G1 | -Hospital A | +2011-01-30 | +W6 | +Hospital C | +B_STPHY_AURS | +R | +R | +I | +R | +F | +Gram-positive | +Staphylococcus | +aureus | +TRUE | +|||
2014-08-09 | +G3 | +Hospital D | +B_STRPT_PNMN | +S | +S | +S | +R | +M | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +||||||
2013-10-22 | +I10 | +Hospital B | B_STRPT_PNMN | R | R | -R | +S | R | M | Gram-positive | @@ -1019,50 +1019,50 @@ different bug/drug combinations, you can use the||||||||
E. coli | AMX | -1429 | -1211 | -3174 | -5814 | +1503 | +1236 | +3099 | +5838 | |||||||||
E. coli | AMC | -2674 | -1190 | -1950 | -5814 | +2754 | +1167 | +1917 | +5838 | |||||||||
E. coli | CIP | -2013 | -1796 | -2005 | -5814 | +1994 | +1798 | +2046 | +5838 | |||||||||
E. coli | GEN | -1931 | -1816 | -2067 | -5814 | +1990 | +1840 | +2008 | +5838 | |||||||||
K. pneumoniae | AMX | 0 | 0 | -1299 | -1299 | +1356 | +1356 | |||||||||||
K. pneumoniae | AMC | -589 | -258 | -452 | -1299 | +585 | +293 | +478 | +1356 |
proportion_SI()
, equa
own:
data_1st %>% resistance(AMX)
-# [1] 0.5895247
Or can be used in conjunction with group_by()
and
summarise()
, both from the dplyr
package:
@@ -1158,19 +1158,19 @@ own:Hospital A -0.5991561 +0.5942184 Hospital B -0.5865273 +0.5841676 Hospital C -0.5910560 +0.5905338 @@ -1195,23 +1195,23 @@ all isolates available for every group (i.e. values S, I or R): Hospital D -0.5797160 +0.5620063 Hospital A -0.5991561 -3555 +0.5942184 +3736 Hospital B -0.5865273 -4305 +0.5841676 +4295 Hospital C -0.5910560 -1856 +0.5905338 +1817 @@ -1236,27 +1236,27 @@ therapies very easily: Hospital D -0.5797160 -2465 +0.5620063 +2532 Escherichia -0.6646027 -0.6444788 -0.8778810 +0.6716341 +0.6560466 +0.8859198 Klebsiella -0.6520400 -0.6574288 -0.8760585 +0.6474926 +0.6438053 +0.8753687 Staphylococcus -0.6681008 -0.6653350 -0.8899816 +0.6660606 +0.6512121 +0.8875758 @@ -1284,23 +1284,23 @@ classes, use a antibiotic class selector such as Streptococcus -0.4751929 +0.4729586 0.0000000 -0.4751929 +0.4729586 Hospital A -59.9% -35.9% +59.4% +36.3% Hospital B -58.7% -36.4% +58.4% +36.3% Hospital C 59.1% -37.4% +38.5% @@ -1416,18 +1416,16 @@ classes) Hospital D -58.0% -36.4% +56.2% +34.7% <mic>
and<disk>
:mic_values <- random_mic(size = 100) mic_values # Class 'mic' -# [1] 0.025 <=0.001 <=0.001 32 0.01 4 0.002 0.125 0.01 -# [10] 32 0.002 0.125 0.005 0.5 1 2 16 4 -# [19] <=0.001 0.25 0.125 128 <=0.001 0.005 >=256 64 16 -# [28] 32 0.025 8 0.125 1 0.25 64 0.0625 0.25 -# [37] 0.5 0.5 16 0.002 0.002 0.5 0.005 16 0.25 -# [46] 0.125 8 <=0.001 1 0.025 <=0.001 0.5 8 16 -# [55] 1 16 8 0.002 0.5 0.5 128 16 >=256 -# [64] 2 0.005 0.01 4 8 0.0625 0.125 0.125 0.125 -# [73] 16 0.002 0.01 8 1 8 0.125 2 32 -# [82] 0.0625 >=256 4 0.005 128 0.025 1 128 0.005 -# [91] >=256 0.025 32 8 <=0.001 <=0.001 <=0.001 1 0.025 -# [100] 0.01
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
# Class 'disk'
-# [1] 22 28 30 21 25 20 18 28 17 29 29 23 17 17 21 18 17 17 23 20 21 21 23 28 29
-# [26] 18 19 31 17 20 26 29 27 29 18 30 21 30 28 20 26 28 30 30 23 31 20 22 25 30
-# [51] 22 19 25 25 26 21 22 23 22 24 24 27 23 29 30 26 18 24 31 29 30 31 19 25 22
-# [76] 28 20 18 31 17 18 23 27 23 26 28 22 28 18 25 22 28 24 31 26 25 18 30 18 21
+# [1] 22 25 18 25 31 22 24 27 25 17 20 31 24 28 26 23 19 28 19 23 29 29 17 25 22
+# [26] 17 18 18 26 27 28 19 27 24 22 23 18 29 19 25 24 18 21 17 17 29 18 25 28 29
+# [51] 22 20 27 21 27 27 31 31 18 22 20 26 24 20 25 28 25 20 19 28 30 19 28 19 23
+# [76] 28 28 27 21 23 27 21 31 23 30 31 19 25 31 25 30 22 28 29 31 28 21 22 25 21
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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