From 8438e68df5398777ab99f7d431f66a91846d2915 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat, 22 Oct 2022 20:10:04 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9033@c2801ba --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 520 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 38802 -> 39243 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 56817 -> 54896 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 28420 -> 28089 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 35866 -> 36460 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 38230 -> 38871 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 49200 -> 49975 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 43354 -> 43067 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28427 -> 28459 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78108 -> 78003 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49896 -> 49852 bytes articles/EUCAST.html | 2 +- articles/MDR.html | 58 +- articles/PCA.html | 2 +- articles/SPSS.html | 2 +- articles/WHONET.html | 18 +- articles/datasets.html | 56 +- articles/index.html | 2 +- articles/resistance_predict.html | 2 +- articles/welcome_to_AMR.html | 4 +- authors.html | 2 +- index.html | 6 +- news/index.html | 20 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR.html | 8 +- reference/Rplot005.png | Bin 13415 -> 13248 bytes reference/Rplot006.png | Bin 12945 -> 12790 bytes reference/Rplot007.png | Bin 13528 -> 12747 bytes reference/Rplot008.png | Bin 17004 -> 16721 bytes reference/Rplot009.png | Bin 8660 -> 8616 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/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.disk.html | 2 +- reference/as.mic.html | 13 +- reference/as.mo.html | 2 +- reference/as.rsi.html | 43 +- reference/atc_online.html | 2 +- reference/availability.html | 2 +- reference/bug_drug_combinations.html | 6 +- 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 | 128 ++--- reference/ggplot_pca.html | 2 +- reference/ggplot_rsi.html | 2 +- reference/guess_ab_col.html | 2 +- reference/index.html | 6 +- reference/intrinsic_resistant.html | 2 +- reference/italicise_taxonomy.html | 2 +- reference/join.html | 30 +- reference/key_antimicrobials.html | 2 +- reference/kurtosis.html | 6 +- reference/like.html | 2 +- reference/mdro.html | 2 +- reference/mean_amr_distance.html | 79 ++- reference/microorganisms.codes.html | 12 +- reference/microorganisms.html | 42 +- 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 26851 -> 26551 bytes reference/plot-2.png | Bin 27306 -> 27127 bytes reference/plot-3.png | Bin 27304 -> 27775 bytes reference/plot-4.png | Bin 38607 -> 38547 bytes reference/plot-5.png | Bin 39079 -> 38871 bytes reference/plot-6.png | Bin 37772 -> 37628 bytes reference/plot-7.png | Bin 37969 -> 34929 bytes reference/plot-8.png | Bin 53860 -> 52869 bytes reference/plot-9.png | Bin 26427 -> 26443 bytes reference/plot.html | 4 +- reference/proportion.html | 2 +- reference/random.html | 35 +- reference/resistance_predict.html | 2 +- reference/rsi_translation.html | 36 +- reference/skewness.html | 4 +- reference/translate.html | 2 +- search.json | 2 +- 94 files changed, 632 insertions(+), 618 deletions(-) diff --git a/404.html b/404.html index 9460d6ec..aa910b35 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 1.8.2.9032 + 1.8.2.9033
So only 53.6% is suitable for resistance analysis! We can now filter on it with the filter()
function, also from the dplyr
package:
@@ -499,10 +499,10 @@ Longest: 1
data_1st <- data %>%
filter_first_isolate()
# Including isolates from ICU.
So we end up with 10,729 isolates for analysis. Now our data looks like:
+So we end up with 10,719 isolates for analysis. Now our data looks like:
head(data_1st)
2 | -2013-04-01 | -U4 | -Hospital D | +1 | +2010-01-20 | +Z10 | +Hospital C | B_ESCHR_COLI | S | S | @@ -553,30 +553,14 @@ Longest: 1TRUE | ||||||||||
3 | -2013-08-12 | -S7 | -Hospital B | -B_ESCHR_COLI | -R | -R | -S | -S | -F | -Gram-negative | -Escherichia | -coli | -TRUE | -||||||||
4 | -2014-05-02 | -K4 | -Hospital B | +2014-11-04 | +C6 | +Hospital C | B_ESCHR_COLI | -R | -I | -R | +S | +S | +S | S | M | Gram-negative | @@ -584,49 +568,65 @@ Longest: 1coli | TRUE | |||
5 | -2016-07-08 | -E6 | -Hospital B | -B_STPHY_AURS | -S | -S | -S | -S | -M | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -||||||||
7 | -2017-02-23 | -B4 | -Hospital D | -B_STPHY_AURS | -R | -R | -R | -R | -M | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -||||||||
9 | -2016-11-10 | -V1 | -Hospital B | -B_STPHY_AURS | -R | +2011-08-14 | +S4 | +Hospital C | +B_ESCHR_COLI | +S | S | R | S | F | +Gram-negative | +Escherichia | +coli | +TRUE | +|||
11 | +2013-07-11 | +X7 | +Hospital C | +B_ESCHR_COLI | +R | +S | +S | +S | +F | +Gram-negative | +Escherichia | +coli | +TRUE | +||||||||
13 | +2013-09-05 | +O5 | +Hospital D | +B_STRPT_PNMN | +S | +S | +S | +R | +F | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +||||||||
14 | +2016-11-07 | +H9 | +Hospital A | +B_STPHY_AURS | +S | +S | +R | +S | +M | Gram-positive | Staphylococcus | aureus | @@ -653,8 +653,8 @@ Longest: 1|||||||||
1 | Escherichia coli | -4,633 | -43.18% | -4,633 | -43.18% | +4,673 | +43.60% | +4,673 | +43.60% | ||||||||||||
2 | Staphylococcus aureus | -2,796 | -26.06% | -7,429 | -69.24% | +2,754 | +25.69% | +7,427 | +69.29% | ||||||||||||
3 | Streptococcus pneumoniae | -2,137 | -19.92% | -9,566 | -89.16% | +2,094 | +19.54% | +9,521 | +88.82% | ||||||||||||
4 | Klebsiella pneumoniae | -1,163 | -10.84% | -10,729 | +1,198 | +11.18% | +10,719 | 100.00% | |||||||||||||
2017-02-23 | -B4 | +2013-09-05 | +O5 | Hospital D | -B_STPHY_AURS | +B_STRPT_PNMN | +S | +S | +S | R | -R | -R | -R | -M | +F | Gram-positive | -Staphylococcus | -aureus | +Streptococcus | +pneumoniae | TRUE |
2016-01-27 | -M1 | +2017-10-30 | +K1 | Hospital B | B_STRPT_PNMN | R | @@ -774,39 +774,39 @@ Longest: 24TRUE | ||||||||||||||
2012-07-10 | -U10 | +2012-03-15 | +L1 | Hospital D | -B_STRPT_PNMN | +B_KLBSL_PNMN | +R | S | S | R | -R | -F | -Gram-positive | -Streptococcus | +M | +Gram-negative | +Klebsiella | pneumoniae | TRUE | ||
2017-03-06 | -X10 | -Hospital D | +2014-11-12 | +E8 | +Hospital A | B_ESCHR_COLI | -S | -S | +I | S | R | -F | +R | +M | Gram-negative | Escherichia | coli | TRUE | |||
2017-08-29 | -F1 | -Hospital B | +2015-08-26 | +A3 | +Hospital C | B_STRPT_PNMN | R | R | @@ -819,8 +819,8 @@ Longest: 24TRUE | ||||||||||||
2014-05-24 | -N8 | +2012-07-18 | +R9 | Hospital B | B_STRPT_PNMN | S | @@ -854,50 +854,50 @@ Longest: 24|||||||||||||||
E. coli | AMX | -2202 | -119 | -2312 | -4633 | +2221 | +115 | +2337 | +4673 | ||||||||||||
E. coli | AMC | -3411 | -175 | -1047 | -4633 | +3415 | +161 | +1097 | +4673 | ||||||||||||
E. coli | CIP | -3383 | +3488 | 0 | -1250 | -4633 | +1185 | +4673 | |||||||||||||
E. coli | GEN | -4044 | +4081 | 0 | -589 | -4633 | +592 | +4673 | |||||||||||||
K. pneumoniae | AMX | 0 | 0 | -1163 | -1163 | +1198 | +1198 | ||||||||||||||
K. pneumoniae | AMC | -917 | -41 | -205 | -1163 | +959 | +35 | +204 | +1198 |
As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (proportion_R()
, equal to resistance()
) and susceptibility as the proportion of S and I (proportion_SI()
, equal to susceptibility()
). These functions can be used on their own:
data_1st %>% resistance(AMX)
-# [1] 0.5444123
Or can be used in conjunction with group_by()
and summarise()
, both from the dplyr
package:
data_1st %>%
@@ -975,19 +975,19 @@ Longest: 24
Hospital A
-0.5464199
+0.5483379
Hospital B
-0.5451604
+0.5483871
Hospital C
-0.5317705
+0.5518331
Hospital D
-0.5496909
+0.5542563
@@ -1008,23 +1008,23 @@ Longest: 24
Hospital A
-0.5464199
-3296
+0.5483379
+3279
Hospital B
-0.5451604
-3709
+0.5483871
+3720
Hospital C
-0.5317705
-1621
+0.5518331
+1582
Hospital D
-0.5496909
-2103
+0.5542563
+2138
@@ -1047,27 +1047,27 @@ Longest: 24
Escherichia
-0.7740125
-0.8728686
-0.9769048
+0.7652472
+0.8733148
+0.9736786
Klebsiella
-0.8237317
-0.8899398
-0.9724850
+0.8297162
+0.8923205
+0.9774624
Staphylococcus
-0.7914878
-0.8884120
-0.9846209
+0.7803195
+0.8863471
+0.9803922
Streptococcus
-0.5297146
+0.5272206
0.0000000
-0.5297146
+0.5272206
@@ -1092,23 +1092,23 @@ Longest: 24
Hospital A
-54.6%
-27.2%
+54.8%
+26.2%
Hospital B
-54.5%
-26.0%
+54.8%
+27.2%
Hospital C
-53.2%
-25.6%
+55.2%
+27.4%
Hospital D
-55.0%
-26.9%
+55.4%
+27.7%
@@ -1206,18 +1206,16 @@ Longest: 24
mic_values <- random_mic(size = 100)
mic_values
# Class 'mic'
-# [1] <=0.001 2 0.25 0.002 0.0625 1 0.002 32 1
-# [10] 0.5 1 0.025 0.5 <=0.001 0.005 4 >=256 4
-# [19] 8 1 16 0.002 <=0.001 0.002 4 0.025 8
-# [28] 16 16 1 0.25 <=0.001 16 0.005 0.005 <=0.001
-# [37] <=0.001 16 >=256 16 128 0.0625 1 0.25 0.005
-# [46] 0.01 0.002 0.5 128 64 0.01 8 128 1
-# [55] >=256 >=256 1 0.125 <=0.001 0.25 64 2 0.002
-# [64] >=256 16 1 >=256 0.5 8 >=256 >=256 0.005
-# [73] 0.002 2 0.25 0.25 <=0.001 0.0625 0.01 0.125 1
-# [82] 0.005 0.125 0.25 2 0.025 0.025 32 1 0.25
-# [91] 0.005 0.01 1 0.5 1 0.0625 0.5 4 1
-# [100] 64
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
# Class 'disk'
-# [1] 27 30 17 21 31 26 25 21 24 31 20 28 23 26 30 22 30 17 23 29 24 30 23 26 19
-# [26] 29 24 23 19 19 30 27 23 31 27 26 24 27 26 20 17 22 29 17 23 20 19 26 28 30
-# [51] 21 30 23 30 30 17 26 25 30 20 24 27 24 20 28 23 22 22 29 18 20 27 22 22 17
-# [76] 30 19 27 27 23 19 23 31 19 26 30 25 22 23 27 28 19 29 19 19 26 26 17 23 17
+# [1] 29 28 23 31 30 24 29 31 28 24 25 28 30 25 27 21 31 23 30 19 22 28 26 24 28
+# [26] 22 27 28 31 20 24 22 26 17 27 17 17 25 27 23 24 20 26 27 17 22 21 17 23 26
+# [51] 18 25 22 17 24 23 29 20 20 22 19 18 26 28 18 23 28 21 29 23 20 30 19 26 29
+# [76] 19 25 29 23 30 23 26 20 19 27 18 31 29 19 20 17 25 29 23 27 18 28 17 22 28
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")