From 8685119254453868bda586d44faa911757c1d649 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat, 18 Feb 2023 14:06:39 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9137@380cbec --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 492 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 39102 -> 38759 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 51147 -> 56319 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 27754 -> 28086 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 36527 -> 39111 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 38149 -> 38816 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 50997 -> 50844 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 41773 -> 42052 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28442 -> 28418 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78297 -> 78229 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49822 -> 49897 bytes articles/EUCAST.html | 2 +- articles/MDR.html | 62 +-- articles/PCA.html | 4 +- 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 13284 -> 13278 bytes reference/Rplot006.png | Bin 12818 -> 12816 bytes reference/Rplot007.png | Bin 13026 -> 13683 bytes reference/Rplot008.png | Bin 16725 -> 16702 bytes reference/Rplot009.png | Bin 8534 -> 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/antibiogram.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 | 117 +++-- 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 | 72 +-- 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 26873 -> 27279 bytes reference/plot-2.png | Bin 27142 -> 27156 bytes reference/plot-3.png | Bin 27742 -> 28569 bytes reference/plot-4.png | Bin 38860 -> 38990 bytes reference/plot-5.png | Bin 38831 -> 38827 bytes reference/plot-6.png | Bin 37606 -> 37590 bytes reference/plot-7.png | Bin 35930 -> 38432 bytes reference/plot-8.png | Bin 52860 -> 52990 bytes reference/plot-9.png | Bin 26123 -> 26145 bytes reference/plot.html | 2 +- reference/proportion.html | 2 +- reference/random.html | 35 +- reference/resistance_predict.html | 2 +- reference/skewness.html | 4 +- reference/translate.html | 2 +- search.json | 2 +- 100 files changed, 496 insertions(+), 496 deletions(-) diff --git a/404.html b/404.html index b420a9bc..be9635a7 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 1.8.2.9135 + 1.8.2.9137
So only 61.4% is suitable for resistance analysis! We can now filter +
So only 61.6% 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 12 281 isolates for analysis. Now our data looks +
So we end up with 12 322 isolates for analysis. Now our data looks like:
head(data_1st)
1 | -2013-03-07 | -S9 | -Hospital A | -B_STRPT_PNMN | -R | -R | -S | -R | -F | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -|||||||||
2 | -2016-12-05 | +2011-07-03 | F3 | -Hospital A | +Hospital D | B_ESCHR_COLI | -R | -R | +S | +S | I | S | M | @@ -711,30 +695,30 @@ like:coli | TRUE | |||||||
3 | -2010-02-20 | -C1 | -Hospital D | +2015-06-20 | +R4 | +Hospital B | B_STRPT_PNMN | -I | -I | +R | +R | S | R | -M | +F | Gram-positive | Streptococcus | pneumoniae | TRUE | |||
5 | -2013-01-12 | -R6 | +||||||||||||||||||||
4 | +2012-08-20 | +U4 | Hospital B | B_ESCHR_COLI | -R | -R | +S | +S | I | S | F | @@ -743,32 +727,48 @@ like:coli | TRUE | |||||||||
6 | -2017-02-28 | -B3 | +||||||||||||||||||||
7 | +2017-10-28 | +J6 | Hospital B | B_ESCHR_COLI | R | R | -I | -I | +S | +S | M | Gram-negative | Escherichia | coli | TRUE | |||||||
8 | +2017-08-19 | +I1 | +Hospital D | +B_STPHY_AURS | +R | +R | +R | +S | +M | +Gram-positive | +Staphylococcus | +aureus | +TRUE | +|||||||||
9 | -2014-07-31 | -Y4 | +2017-07-16 | +S8 | Hospital B | B_ESCHR_COLI | R | +R | I | I | -S | F | Gram-negative | Escherichia | @@ -808,8 +808,8 @@ readable:1 | Escherichia coli | 5,843 | -47.58% | +47.42% | 5,843 | -47.58% | +47.42% |
2 | Staphylococcus aureus | -3,269 | -26.62% | -9,112 | -74.20% | +3,319 | +26.94% | +9,162 | +74.35% | |||||||||||||
3 | Streptococcus pneumoniae | -1,832 | -14.92% | -10,944 | -89.11% | +1,857 | +15.07% | +11,019 | +89.43% | |||||||||||||
4 | Klebsiella pneumoniae | -1,337 | -10.89% | -12,281 | +1,303 | +10.57% | +12,322 | 100.00% | ||||||||||||||
2013-03-07 | -S9 | -Hospital A | -B_STRPT_PNMN | -R | -R | -S | -R | -F | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -||||||||||
2010-02-20 | -C1 | -Hospital D | -B_STRPT_PNMN | -I | -I | -S | -R | -M | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -||||||||||
2013-12-08 | -S8 | +2015-06-20 | +R4 | Hospital B | B_STRPT_PNMN | -I | -I | +R | +R | S | R | F | @@ -954,13 +924,43 @@ antibiotic class they are in:TRUE | |||||||||
2012-07-08 | -C6 | -Hospital D | +2014-01-08 | +V3 | +Hospital C | +B_STPHY_AURS | +R | +R | +S | +R | +F | +Gram-positive | +Staphylococcus | +aureus | +TRUE | +|||||||
2013-07-30 | +Y4 | +Hospital B | +B_ESCHR_COLI | +I | +I | +I | +R | +F | +Gram-negative | +Escherichia | +coli | +TRUE | +||||||||||
2013-03-23 | +E6 | +Hospital A | B_STRPT_PNMN | S | S | -S | +I | R | M | Gram-positive | @@ -969,33 +969,33 @@ antibiotic class they are in:TRUE | |||||||||||
2011-06-17 | -G10 | -Hospital C | -B_STRPT_PNMN | -I | -I | +2013-12-04 | +S8 | +Hospital B | +B_ESCHR_COLI | +R | S | R | -M | -Gram-positive | -Streptococcus | -pneumoniae | +R | +F | +Gram-negative | +Escherichia | +coli | TRUE |
2011-06-11 | -N7 | +2013-02-27 | +Z2 | Hospital A | -B_STRPT_PNMN | +B_STPHY_AURS | +R | +R | I | -I | -S | R | F | Gram-positive | -Streptococcus | -pneumoniae | +Staphylococcus | +aureus | TRUE | |||
E. coli | AMC | -2674 | -1181 | -1988 | +2759 | +1167 | +1917 | 5843 | ||||||||||||||
E. coli | AMX | -1496 | -1187 | -3160 | +1459 | +1245 | +3139 | 5843 | ||||||||||||||
E. coli | CIP | -2028 | -1831 | +2071 | +1788 | 1984 | 5843 | |||||||||||||||
E. coli | GEN | -2077 | -1762 | -2004 | +2002 | +1833 | +2008 | 5843 | ||||||||||||||
K. pneumoniae | AMC | -573 | -303 | -461 | -1337 | +583 | +292 | +428 | +1303 | |||||||||||||
K. pneumoniae | AMX | 0 | 0 | -1337 | -1337 | +1303 | +1303 |
proportion_SI()
, equa
own:
data_1st %>% resistance(AMX)
-#> [1] 0.5882257
Or can be used in conjunction with group_by()
and
summarise()
, both from the dplyr
package:
@@ -1159,19 +1159,19 @@ own:Hospital A -0.5913304 +0.5827676 Hospital B -0.5810277 +0.5907183 Hospital C -0.6058002 +0.5845813 @@ -1196,23 +1196,23 @@ all isolates available for every group (i.e. values S, I or R): Hospital D -0.5828571 +0.5747605 Hospital A -0.5913304 -3668 +0.5827676 +3830 Hospital B -0.5810277 -4301 +0.5907183 +4288 Hospital C -0.6058002 -1862 +0.5845813 +1803 @@ -1237,27 +1237,27 @@ therapies very easily: Hospital D -0.5828571 -2450 +0.5747605 +2401 Escherichia -0.6597638 -0.6570255 -0.8873866 +0.6719151 +0.6563409 +0.8921787 Klebsiella -0.6551982 -0.6641735 -0.8840688 +0.6715272 +0.6745971 +0.8879509 Staphylococcus -0.6628939 -0.6570817 -0.8877333 +0.6776137 +0.6595360 +0.8945466 @@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as Streptococcus -0.4737991 +0.4717286 0.0000000 -0.4737991 +0.4717286 Hospital A -59.1% -37.7% +58.3% +35.1% Hospital B -58.1% -35.5% +59.1% +35.8% Hospital C -60.6% -37.3% +58.5% +37.4% @@ -1417,16 +1417,16 @@ classes) Hospital D -58.3% -37.1% +57.5% +34.9% <mic>
and<disk>
:mic_values <- random_mic(size = 100) mic_values #> Class 'mic' -#> [1] 1 8 0.01 8 0.01 0.001 1 0.0625 0.01 0.002 -#> [11] 0.0625 8 128 0.005 0.001 32 1 0.0625 64 256 -#> [21] 4 0.002 1 0.0625 0.001 0.25 4 4 0.002 8 -#> [31] 64 1 4 0.01 128 1 0.002 0.01 0.5 0.25 -#> [41] 0.0625 0.005 256 1 2 32 0.01 128 0.002 64 -#> [51] 0.5 0.5 32 16 0.002 0.5 32 0.125 0.0625 0.001 -#> [61] 32 0.125 0.002 256 2 0.0625 0.002 0.025 0.025 0.001 -#> [71] 0.0625 16 256 16 2 4 8 0.001 0.025 0.125 -#> [81] 1 0.01 8 0.125 0.5 2 128 0.005 256 0.125 -#> [91] 8 0.25 0.005 0.25 0.002 2 32 0.125 4 0.025
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
#> Class 'disk'
-#> [1] 23 29 25 27 30 18 31 23 27 29 30 26 26 17 24 27 22 23 28 17 27 21 31 23 31
-#> [26] 28 19 23 28 22 26 25 30 20 20 23 30 31 27 22 20 28 22 28 20 20 29 20 31 22
-#> [51] 24 27 19 25 31 21 17 21 29 24 27 27 31 26 17 22 26 26 26 31 20 31 23 31 21
-#> [76] 18 19 31 28 25 25 31 29 29 17 23 22 29 23 30 23 23 31 19 18 28 20 31 22 19
+#> [1] 28 18 29 27 31 26 27 30 31 18 30 25 17 20 20 31 22 22 30 26 24 26 23 28 28
+#> [26] 24 27 29 20 30 25 25 25 22 23 27 27 23 29 27 23 20 19 23 23 18 29 21 31 29
+#> [51] 19 31 27 27 31 20 22 28 31 19 21 30 28 21 24 21 20 20 19 27 26 30 19 24 29
+#> [76] 17 26 18 27 23 19 29 24 27 27 20 25 28 17 21 29 29 17 22 20 26 24 23 17 25
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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