From fefbb46ec6aa5429bce7b0f612317ab48c8da943 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 22 Feb 2023 15:34:03 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9141@a84101d --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 552 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 39313 -> 39310 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 53879 -> 52261 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 27852 -> 27863 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 41586 -> 41338 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 39031 -> 38103 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 49778 -> 51602 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 42055 -> 41927 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28431 -> 28460 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78270 -> 78281 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49903 -> 49884 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 | 26 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR-options.html | 2 +- reference/AMR.html | 2 +- reference/Rplot005.png | Bin 13256 -> 13285 bytes reference/Rplot006.png | Bin 12793 -> 12823 bytes reference/Rplot007.png | Bin 12534 -> 12638 bytes reference/Rplot008.png | Bin 16621 -> 16786 bytes reference/Rplot009.png | Bin 8492 -> 8523 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.html | 39 +- 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 | 110 ++-- 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 25876 -> 25929 bytes reference/plot-2.png | Bin 27123 -> 27137 bytes reference/plot-3.png | Bin 28338 -> 27781 bytes reference/plot-4.png | Bin 37804 -> 37848 bytes reference/plot-5.png | Bin 38786 -> 38811 bytes reference/plot-6.png | Bin 37556 -> 37572 bytes reference/plot-7.png | Bin 36417 -> 36986 bytes reference/plot-8.png | Bin 52870 -> 53007 bytes reference/plot-9.png | Bin 26196 -> 26122 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 | 2 +- search.json | 2 +- 100 files changed, 538 insertions(+), 542 deletions(-) diff --git a/404.html b/404.html index bbd5368d..708d238e 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 1.8.2.9140 + 1.8.2.9141
So only 61.5% is suitable for resistance analysis! We can now filter +
So only 61.8% 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 12 307 isolates for analysis. Now our data looks +
So we end up with 12 352 isolates for analysis. Now our data looks like:
head(data_1st)
1 | -2014-05-20 | -U8 | -Hospital A | -B_STPHY_AURS | -R | -R | -I | -I | -F | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -||
2 | -2017-10-06 | -A7 | -Hospital D | -B_ESCHR_COLI | -R | -I | -I | -I | -M | -Gram-negative | -Escherichia | -coli | -TRUE | -||
3 | -2010-12-13 | -N3 | -Hospital C | -B_ESCHR_COLI | -S | -S | -R | -S | -M | -Gram-negative | -Escherichia | -coli | -TRUE | -||
4 | -2015-01-26 | -S8 | -Hospital B | -B_ESCHR_COLI | -R | -R | -S | -R | -F | -Gram-negative | -Escherichia | -coli | -TRUE | -||
6 | -2011-08-06 | -N5 | +2017-11-27 | +L9 | Hospital B | B_STPHY_AURS | S | @@ -761,20 +697,84 @@ like:||||||||
7 | -2014-05-14 | -C6 | +2010-03-27 | +Y9 | Hospital B | B_ESCHR_COLI | R | R | +R | +I | +F | +Gram-negative | +Escherichia | +coli | +TRUE | +
8 | +2012-08-01 | +G7 | +Hospital B | +B_STPHY_AURS | S | S | +I | +R | +M | +Gram-positive | +Staphylococcus | +aureus | +TRUE | +||
10 | +2015-05-06 | +T1 | +Hospital A | +B_STPHY_AURS | +I | +I | +R | +R | +F | +Gram-positive | +Staphylococcus | +aureus | +TRUE | +||
12 | +2017-02-03 | +I2 | +Hospital A | +B_ESCHR_COLI | +I | +I | +S | +I | M | Gram-negative | Escherichia | coli | TRUE | ||
14 | +2014-02-20 | +C1 | +Hospital B | +B_STRPT_PNMN | +R | +R | +R | +R | +M | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +
Time for the analysis!
@@ -808,8 +808,8 @@ readable:data_1st %>% freq(genus, species)
Frequency table
Class: character
-Length: 12,307
-Available: 12,307 (100%, NA: 0 = 0%)
+Length: 12,352
+Available: 12,352 (100%, NA: 0 = 0%)
Unique: 4
Shortest: 16
Longest: 24
proportion_SI()
, equa
own:
data_1st %>% resistance(AMX)
-#> [1] 0.5778013
Or can be used in conjunction with group_by()
and
summarise()
, both from the dplyr
package:
@@ -1159,19 +1159,19 @@ own:Hospital A -0.5752970 +0.5857797 Hospital B -0.5688009 +0.5846154 Hospital C -0.5894074 +0.5920836 @@ -1196,23 +1196,23 @@ all isolates available for every group (i.e. values S, I or R): Hospital D -0.5880933 +0.5768763 Hospital A -0.5752970 -3619 +0.5857797 +3713 Hospital B -0.5688009 -4295 +0.5846154 +4355 Hospital C -0.5894074 -1907 +0.5920836 +1819 @@ -1237,27 +1237,27 @@ therapies very easily: Hospital D -0.5880933 -2486 +0.5768763 +2465 Escherichia -0.6707005 -0.6499063 -0.8813704 +0.6661088 +0.6510460 +0.8816736 Klebsiella -0.6616990 -0.6721311 -0.8964232 +0.6430769 +0.6546154 +0.8792308 Staphylococcus -0.6726718 -0.6622901 -0.8934351 +0.6634496 +0.6534869 +0.8826276 @@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as Streptococcus -0.4816237 +0.4734584 0.0000000 -0.4816237 +0.4734584 Hospital A -57.5% -35.3% +58.6% +37.9% Hospital B -56.9% -35.1% +58.5% +34.9% Hospital C -58.9% -36.8% +59.2% +38.1% @@ -1417,18 +1417,18 @@ classes) Hospital D -58.8% -36.8% +57.7% +36.7% <mic>
and<disk>
:mic_values <- random_mic(size = 100) mic_values #> Class 'mic' -#> [1] 16 32 8 4 0.125 0.25 16 64 16 -#> [10] 4 4 <=0.001 2 0.25 0.125 0.0625 128 0.01 -#> [19] 0.025 >=256 1 0.025 128 0.125 128 0.25 0.005 -#> [28] >=256 4 16 0.01 0.005 >=256 8 0.002 64 -#> [37] 0.025 0.002 <=0.001 1 0.25 4 0.005 0.01 0.005 -#> [46] 32 0.125 1 2 >=256 0.01 0.025 0.5 64 -#> [55] 16 0.01 2 8 1 4 32 64 >=256 -#> [64] 64 8 0.125 0.01 0.5 32 32 0.25 128 -#> [73] 0.01 0.01 4 0.125 64 32 0.002 32 32 -#> [82] 0.01 0.25 1 <=0.001 32 0.01 0.025 0.25 64 -#> [91] 0.0625 0.005 0.01 0.25 <=0.001 0.25 0.125 0.0625 0.01 -#> [100] 2
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
#> Class 'disk'
-#> [1] 19 18 19 22 17 21 31 27 23 29 26 25 28 19 30 27 20 23 20 21 21 21 29 17 26
-#> [26] 21 24 27 24 25 25 29 26 23 23 20 30 23 30 24 20 22 19 18 23 24 25 22 23 22
-#> [51] 17 17 25 22 31 19 20 28 21 28 24 22 23 17 28 30 28 27 22 27 27 17 30 31 17
-#> [76] 27 25 23 17 27 25 28 18 18 29 26 22 22 20 30 20 29 25 26 29 20 28 30 24 27
+#> [1] 21 17 22 25 18 19 27 23 26 29 23 21 31 23 18 23 19 21 28 24 22 19 19 28 17
+#> [26] 18 29 29 21 26 25 29 17 26 31 28 22 17 31 28 21 21 30 25 20 30 27 19 21 18
+#> [51] 23 18 27 23 18 19 24 27 21 20 25 27 18 17 23 23 31 23 22 26 20 29 28 21 26
+#> [76] 17 18 18 19 19 17 21 20 18 25 21 23 28 25 18 18 28 18 27 18 22 23 18 19 24
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")