From 1fe0350d1538899167877cc54f145321e4ce8a63 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 22 Feb 2023 14:50:02 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9139@c2cfc5e --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 537 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 39287 -> 38760 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 55289 -> 56650 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 27745 -> 27731 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 36580 -> 38074 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 38574 -> 38822 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 49585 -> 49225 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 41510 -> 41766 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28459 -> 28444 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78253 -> 78216 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49910 -> 49776 bytes articles/EUCAST.html | 2 +- articles/MDR.html | 56 +- articles/PCA.html | 2 +- articles/SPSS.html | 2 +- articles/WHONET.html | 15 +- articles/datasets.html | 2 +- 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 13184 -> 13142 bytes reference/Rplot006.png | Bin 12708 -> 12657 bytes reference/Rplot007.png | Bin 13657 -> 12869 bytes reference/Rplot008.png | Bin 17950 -> 17961 bytes reference/Rplot009.png | Bin 8082 -> 8480 bytes reference/WHOCC.html | 2 +- reference/WHONET.html | 11 +- reference/ab_from_text.html | 5 +- reference/ab_property.html | 10 +- reference/add_custom_antimicrobials.html | 18 +- reference/add_custom_microorganisms.html | 2 +- reference/age.html | 22 +- reference/age_groups.html | 2 +- reference/antibiogram-1.png | Bin 15255 -> 26492 bytes reference/antibiogram-2.png | Bin 15454 -> 39648 bytes reference/antibiogram-3.png | Bin 0 -> 24603 bytes reference/antibiogram-4.png | Bin 0 -> 32347 bytes reference/antibiogram.html | 37 +- reference/antibiotic_class_selectors.html | 2 +- reference/antibiotics.html | 2 +- reference/as.ab.html | 7 +- reference/as.av.html | 2 +- reference/as.disk.html | 2 +- reference/as.mic.html | 2 +- reference/as.mo.html | 3 +- 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 | 4 +- 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 | 112 ++-- 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 | 73 +-- 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 27287 -> 26968 bytes reference/plot-2.png | Bin 26491 -> 26535 bytes reference/plot-3.png | Bin 27846 -> 28116 bytes reference/plot-4.png | Bin 38994 -> 38559 bytes reference/plot-5.png | Bin 38171 -> 38201 bytes reference/plot-6.png | Bin 36872 -> 36917 bytes reference/plot-7.png | Bin 38375 -> 35333 bytes reference/plot-8.png | Bin 54792 -> 54772 bytes reference/plot-9.png | Bin 24794 -> 26146 bytes reference/plot.html | 2 +- reference/proportion.html | 2 +- reference/random.html | 36 +- reference/resistance_predict.html | 2 +- reference/skewness.html | 4 +- reference/translate.html | 5 +- search.json | 2 +- 104 files changed, 544 insertions(+), 579 deletions(-) create mode 100644 reference/antibiogram-3.png create mode 100644 reference/antibiogram-4.png diff --git a/404.html b/404.html index 19574612..57f7beaf 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 1.8.2.9138 + 1.8.2.9139
So only 62.2% is suitable for resistance analysis! We can now filter +
So only 61.5% 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 12 431 isolates for analysis. Now our data looks +
So we end up with 12 293 isolates for analysis. Now our data looks like:
head(data_1st)
1 | -2014-12-01 | -V4 | +2011-02-12 | +O4 | Hospital A | -B_ESCHR_COLI | -R | -I | -I | -R | -F | -Gram-negative | -Escherichia | -coli | -TRUE | -||||
2 | -2010-08-12 | -I7 | -Hospital C | -B_STPHY_AURS | -R | -S | -S | -S | -M | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -||||||
3 | -2012-07-28 | -V1 | -Hospital B | B_STRPT_PNMN | -S | -S | -R | +I | +I | +I | R | F | Gram-positive | @@ -728,30 +696,30 @@ like:TRUE | |||||
6 | -2015-05-14 | -N5 | +2 | +2011-03-08 | +W5 | Hospital C | -B_STPHY_AURS | -I | -I | -I | -S | -M | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -|||
7 | -2011-03-07 | -X4 | -Hospital D | B_ESCHR_COLI | I | I | -S | +I | +I | +F | +Gram-negative | +Escherichia | +coli | +TRUE | +|||||
3 | +2015-09-22 | +R6 | +Hospital B | +B_ESCHR_COLI | +R | +R | +R | I | F | Gram-negative | @@ -760,19 +728,51 @@ like:TRUE | ||||||||
8 | -2016-11-12 | -T7 | -Hospital A | -B_KLBSL_PNMN | -R | +6 | +2017-10-13 | +F8 | +Hospital D | +B_ESCHR_COLI | +I | S | I | S | +M | +Gram-negative | +Escherichia | +coli | +TRUE | +
7 | +2013-03-22 | +H3 | +Hospital D | +B_STRPT_PNMN | +R | +R | +I | +R | +M | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +||||||
8 | +2014-11-05 | +Y10 | +Hospital D | +B_ESCHR_COLI | +R | +R | +S | +R | F | Gram-negative | -Klebsiella | -pneumoniae | +Escherichia | +coli | TRUE | ||||
1 | Escherichia coli | -5,970 | -48.03% | -5,970 | -48.03% | +5,873 | +47.78% | +5,873 | +47.78% | ||||||||||
2 | Staphylococcus aureus | -3,335 | -26.83% | -9,305 | -74.85% | +3,225 | +26.23% | +9,098 | +74.01% | ||||||||||
3 | Streptococcus pneumoniae | -1,817 | -14.62% | -11,122 | -89.47% | +1,844 | +15.00% | +10,942 | +89.01% | ||||||||||
4 | Klebsiella pneumoniae | -1,309 | -10.53% | -12,431 | +1,351 | +10.99% | +12,293 | 100.00% | |||||||||||
2014-12-01 | -V4 | +2011-02-12 | +O4 | Hospital A | -B_ESCHR_COLI | +B_STRPT_PNMN | +I | +I | +I | +R | +F | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +||||
2013-03-22 | +H3 | +Hospital D | +B_STRPT_PNMN | +R | R | I | -I | +R | +M | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +||||||
2014-11-05 | +Y10 | +Hospital D | +B_ESCHR_COLI | +R | +R | +S | R | F | Gram-negative | @@ -924,71 +954,41 @@ antibiotic class they are in:TRUE | |||||||||
2012-07-28 | -V1 | +2013-09-13 | +A8 | Hospital B | B_STRPT_PNMN | S | S | R | R | -F | +M | Gram-positive | Streptococcus | pneumoniae | TRUE | ||||
2016-08-30 | -Q3 | +2016-08-04 | +S3 | Hospital D | -B_STRPT_PNMN | -R | -R | +B_STPHY_AURS | R | +I | +I | R | F | Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -||
2013-03-03 | -F7 | -Hospital B | -B_STPHY_AURS | -I | -S | -I | -R | -M | -Gram-positive | Staphylococcus | aureus | TRUE | |||||||
2010-10-30 | -H10 | -Hospital A | -B_STRPT_PNMN | -I | -I | -S | -R | -M | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -|||||||
2011-04-07 | -D8 | +2013-05-16 | +K6 | Hospital C | B_ESCHR_COLI | -S | +I | S | R | R | @@ -1020,50 +1020,50 @@ different bug/drug combinations, you can use the|||||||||
E. coli | AMC | -2855 | -1161 | -1954 | -5970 | +2744 | +1216 | +1913 | +5873 | ||||||||||
E. coli | AMX | -1518 | -1282 | -3170 | -5970 | +1504 | +1272 | +3097 | +5873 | ||||||||||
E. coli | CIP | -2087 | -1796 | -2087 | -5970 | +2018 | +1818 | +2037 | +5873 | ||||||||||
E. coli | GEN | -2119 | -1854 | -1997 | -5970 | +2067 | +1812 | +1994 | +5873 | ||||||||||
K. pneumoniae | AMC | -615 | -256 | -438 | -1309 | +599 | +275 | +477 | +1351 | ||||||||||
K. pneumoniae | AMX | 0 | 0 | -1309 | -1309 | +1351 | +1351 |
proportion_SI()
, equa
own:
data_1st %>% resistance(AMX)
-#> [1] 0.5810474
Or can be used in conjunction with group_by()
and
summarise()
, both from the dplyr
package:
@@ -1159,19 +1159,19 @@ own:Hospital A -0.5871733 +0.5836502 Hospital B -0.5822430 +0.5788257 Hospital C -0.5788635 +0.5675105 @@ -1196,23 +1196,23 @@ all isolates available for every group (i.e. values S, I or R): Hospital D -0.5717638 +0.5893679 Hospital A -0.5871733 -3711 +0.5836502 +3682 Hospital B -0.5822430 -4280 +0.5788257 +4326 Hospital C -0.5788635 -1883 +0.5675105 +1896 @@ -1237,27 +1237,27 @@ therapies very easily: Hospital D -0.5717638 -2557 +0.5893679 +2389 Escherichia -0.6726968 -0.6654941 -0.8934673 +0.6742721 +0.6604802 +0.8923889 Klebsiella -0.6653934 -0.6608098 -0.8800611 +0.6469282 +0.6565507 +0.8793486 Staphylococcus -0.6773613 -0.6587706 -0.8917541 +0.6731783 +0.6536434 +0.8862016 @@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as Streptococcus -0.4777105 +0.4766811 0.0000000 -0.4777105 +0.4766811 Hospital A -58.7% -36.2% +58.4% +36.1% Hospital B -58.2% -35.9% +57.9% +36.2% Hospital C -57.9% -34.9% +56.8% +34.6% @@ -1417,16 +1417,18 @@ classes) Hospital D -57.2% -34.5% +58.9% +35.8% <mic>
and<disk>
:mic_values <- random_mic(size = 100) mic_values #> Class 'mic' -#> [1] 0.0625 0.125 16 0.025 0.005 128 8 4 0.002 32 -#> [11] 64 0.5 0.025 0.01 8 0.002 0.5 1 0.125 0.001 -#> [21] 0.005 0.025 0.005 0.125 0.001 128 0.01 2 64 128 -#> [31] 8 1 1 128 8 4 16 0.5 0.25 0.25 -#> [41] 16 256 0.002 8 0.025 0.5 128 8 256 64 -#> [51] 0.025 128 0.025 0.001 1 0.002 0.125 0.001 256 0.01 -#> [61] 64 0.0625 0.025 16 0.5 0.125 256 1 1 128 -#> [71] 32 0.01 0.01 0.0625 128 4 16 0.005 256 8 -#> [81] 8 0.005 0.01 0.025 32 64 1 0.005 128 0.25 -#> [91] 16 0.001 0.5 0.001 0.25 0.0625 2 2 0.001 0.125
# base R:
plot(mic_values)
<mic>
and <disk>
:
But we could also be more specific, by generating MICs that are likely to be found in E. coli for ciprofloxacin:
-mic_values <- random_mic(size = 100, mo = "E. coli", ab = "cipro")
-#> [1] "here"
mic_values <- random_mic(size = 100, mo = "E. coli", ab = "cipro")
For the plot()
and autoplot()
function, we
can define the microorganism and an antimicrobial agent the same way.
This will add the interpretation of those values according to a chosen
@@ -1461,10 +1462,10 @@ plotting:
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
#> Class 'disk'
-#> [1] 27 29 20 31 27 23 30 27 19 24 31 20 19 28 23 25 17 22 20 24 24 28 17 29 26
-#> [26] 29 31 23 23 30 18 29 30 23 21 19 25 24 22 18 28 25 24 18 25 25 27 24 24 27
-#> [51] 27 18 18 25 22 27 30 24 31 26 19 30 21 22 23 19 23 23 22 26 22 29 29 29 29
-#> [76] 26 26 24 30 17 30 17 25 27 17 27 20 23 17 21 17 27 18 23 30 19 22 20 30 17
+#> [1] 23 21 21 24 27 18 21 29 31 18 17 26 21 21 27 25 28 31 30 17 29 21 18 30 25
+#> [26] 28 31 17 25 23 22 17 27 24 30 31 24 24 25 27 18 31 20 21 29 30 17 21 20 19
+#> [51] 25 21 17 17 26 25 30 26 19 18 21 28 27 21 30 29 21 17 30 28 26 27 23 31 27
+#> [76] 31 31 26 24 30 31 22 20 17 17 23 31 27 17 28 27 18 27 29 24 24 28 20 19 26
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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