From 976d5292c788d547bafe82e49bdbf3c5ef24babf Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 14 Oct 2022 13:52:23 +0000
Subject: [PATCH] Built site for AMR: 1.8.2.9016@85ed7ea
---
articles/AMR.html | 498 +++++++++---------
.../AMR_files/figure-html/disk_plots-1.png | Bin 38742 -> 38411 bytes
.../figure-html/disk_plots_mo_ab-1.png | Bin 56603 -> 53011 bytes
.../AMR_files/figure-html/mic_plots-1.png | Bin 28088 -> 27873 bytes
.../AMR_files/figure-html/mic_plots-2.png | Bin 39095 -> 37627 bytes
.../figure-html/mic_plots_mo_ab-1.png | Bin 38440 -> 39164 bytes
.../figure-html/mic_plots_mo_ab-2.png | Bin 51493 -> 50480 bytes
articles/AMR_files/figure-html/plot 1-1.png | Bin 43269 -> 43283 bytes
articles/AMR_files/figure-html/plot 3-1.png | Bin 28436 -> 28426 bytes
articles/AMR_files/figure-html/plot 4-1.png | Bin 78038 -> 78074 bytes
articles/AMR_files/figure-html/plot 5-1.png | Bin 49864 -> 49879 bytes
articles/MDR.html | 56 +-
articles/datasets.html | 16 +-
pkgdown.yml | 2 +-
reference/Rplot005.png | Bin 13233 -> 12934 bytes
reference/Rplot006.png | Bin 12736 -> 12452 bytes
reference/Rplot007.png | Bin 14682 -> 13592 bytes
reference/Rplot008.png | Bin 20043 -> 19157 bytes
reference/Rplot009.png | Bin 8561 -> 8552 bytes
reference/age.html | 20 +-
reference/as.rsi.html | 20 +-
reference/get_episode.html | 132 +++--
reference/kurtosis.html | 4 +-
reference/mean_amr_distance.html | 78 +--
reference/plot-1.png | Bin 25790 -> 26909 bytes
reference/plot-2.png | Bin 27062 -> 26433 bytes
reference/plot-3.png | Bin 27531 -> 28264 bytes
reference/plot-4.png | Bin 37686 -> 38725 bytes
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reference/plot-7.png | Bin 38859 -> 38025 bytes
reference/plot-8.png | Bin 58693 -> 56834 bytes
reference/plot-9.png | Bin 26126 -> 26284 bytes
reference/random.html | 33 +-
reference/skewness.html | 2 +-
search.json | 2 +-
36 files changed, 430 insertions(+), 433 deletions(-)
diff --git a/articles/AMR.html b/articles/AMR.html
index 3fa02440..a9411b63 100644
--- a/articles/AMR.html
+++ b/articles/AMR.html
@@ -325,19 +325,41 @@
-| 2015-11-18 |
-X2 |
+2017-11-03 |
+T2 |
Hospital A |
-Klebsiella pneumoniae |
-S |
+Escherichia coli |
+R |
S |
S |
S |
F |
-| 2014-12-18 |
-I9 |
+2016-05-27 |
+Z9 |
+Hospital B |
+Staphylococcus aureus |
+S |
+S |
+S |
+S |
+F |
+
+
+| 2015-01-19 |
+N8 |
+Hospital C |
+Escherichia coli |
+I |
+R |
+S |
+S |
+F |
+
+
+| 2017-03-31 |
+G7 |
Hospital C |
Escherichia coli |
S |
@@ -347,48 +369,26 @@
M |
-| 2015-09-24 |
-V4 |
+2014-04-10 |
+C6 |
Hospital A |
-Staphylococcus aureus |
+Streptococcus pneumoniae |
S |
-R |
-S |
-S |
-F |
-
-
-| 2012-11-26 |
-E7 |
-Hospital D |
-Escherichia coli |
-R |
-I |
-S |
-S |
-M |
-
-
-| 2010-08-28 |
-A7 |
-Hospital A |
-Escherichia coli |
-R |
S |
S |
S |
M |
-| 2016-05-06 |
-V5 |
+2011-02-09 |
+N4 |
Hospital A |
Escherichia coli |
S |
-I |
-R |
S |
-F |
+S |
+S |
+M |
@@ -422,16 +422,16 @@ Longest: 1
| 1 |
M |
-10,324 |
-51.62% |
-10,324 |
-51.62% |
+10,375 |
+51.88% |
+10,375 |
+51.88% |
| 2 |
F |
-9,676 |
-48.38% |
+9,625 |
+48.13% |
20,000 |
100.00% |
@@ -488,9 +488,9 @@ Longest: 1
# Basing inclusion on all antimicrobial results, using a points threshold of
# 2
# Including isolates from ICU.
-# => Found 10,765 'phenotype-based' first isolates (53.8% of total where a
+# => Found 10,660 'phenotype-based' first isolates (53.3% of total where a
# microbial ID was available)
-So only 53.8% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:
+So only 53.3% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:
@@ -499,7 +499,7 @@ Longest: 1
data_1st <- data %>%
filter_first_isolate()
# Including isolates from ICU.
-So we end up with 10,765 isolates for analysis. Now our data looks like:
+So we end up with 10,660 isolates for analysis. Now our data looks like:
@@ -537,25 +537,41 @@ Longest: 1
-| 1 |
-2015-11-18 |
-X2 |
-Hospital A |
-B_KLBSL_PNMN |
-R |
+2 |
+2016-05-27 |
+Z9 |
+Hospital B |
+B_STPHY_AURS |
+S |
S |
S |
S |
F |
-Gram-negative |
-Klebsiella |
-pneumoniae |
+Gram-positive |
+Staphylococcus |
+aureus |
TRUE |
-| 2 |
-2014-12-18 |
-I9 |
+3 |
+2015-01-19 |
+N8 |
+Hospital C |
+B_ESCHR_COLI |
+R |
+R |
+S |
+S |
+F |
+Gram-negative |
+Escherichia |
+coli |
+TRUE |
+
+
+| 4 |
+2017-03-31 |
+G7 |
Hospital C |
B_ESCHR_COLI |
S |
@@ -568,62 +584,30 @@ Longest: 1
coli |
TRUE |
-
-| 3 |
-2015-09-24 |
-V4 |
-Hospital A |
-B_STPHY_AURS |
-R |
-R |
-S |
-S |
-F |
-Gram-positive |
-Staphylococcus |
-aureus |
-TRUE |
-
-| 4 |
-2012-11-26 |
-E7 |
-Hospital D |
-B_ESCHR_COLI |
+5 |
+2014-04-10 |
+C6 |
+Hospital A |
+B_STRPT_PNMN |
+S |
+S |
+S |
R |
-I |
-S |
-S |
M |
-Gram-negative |
-Escherichia |
-coli |
+Gram-positive |
+Streptococcus |
+pneumoniae |
TRUE |
| 6 |
-2016-05-06 |
-V5 |
+2011-02-09 |
+N4 |
Hospital A |
B_ESCHR_COLI |
S |
S |
-R |
-S |
-F |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
-| 7 |
-2011-03-21 |
-N1 |
-Hospital D |
-B_ESCHR_COLI |
-S |
-S |
S |
S |
M |
@@ -632,6 +616,22 @@ Longest: 1
coli |
TRUE |
+
+| 10 |
+2010-07-27 |
+E4 |
+Hospital D |
+B_STPHY_AURS |
+R |
+S |
+R |
+S |
+M |
+Gram-positive |
+Staphylococcus |
+aureus |
+TRUE |
+
Time for the analysis!
@@ -653,8 +653,8 @@ Longest: 1
data_1st %>% freq(genus, species)
Frequency table
Class: character
-Length: 10,765
-Available: 10,765 (100.0%, NA: 0 = 0.0%)
+Length: 10,660
+Available: 10,660 (100.0%, NA: 0 = 0.0%)
Unique: 4
Shortest: 16
Longest: 24
@@ -671,33 +671,33 @@ Longest: 24
| 1 |
Escherichia coli |
-4,655 |
-43.24% |
-4,655 |
-43.24% |
+4,666 |
+43.77% |
+4,666 |
+43.77% |
| 2 |
Staphylococcus aureus |
-2,771 |
-25.74% |
-7,426 |
-68.98% |
+2,717 |
+25.49% |
+7,383 |
+69.26% |
| 3 |
Streptococcus pneumoniae |
-2,156 |
-20.03% |
-9,582 |
-89.01% |
+2,101 |
+19.71% |
+9,484 |
+88.97% |
| 4 |
Klebsiella pneumoniae |
-1,183 |
-10.99% |
-10,765 |
+1,176 |
+11.03% |
+10,660 |
100.00% |
@@ -716,14 +716,14 @@ Longest: 24
-
+
-
+
@@ -744,27 +744,27 @@ Longest: 24
-| 2016-02-22 |
-Y6 |
-Hospital D |
-B_STPHY_AURS |
-R |
-R |
+2014-04-10 |
+C6 |
+Hospital A |
+B_STRPT_PNMN |
+S |
+S |
S |
R |
-F |
+M |
Gram-positive |
-Staphylococcus |
-aureus |
+Streptococcus |
+pneumoniae |
TRUE |
-| 2012-04-22 |
-E8 |
+2012-08-04 |
+I5 |
Hospital D |
B_ESCHR_COLI |
-S |
-S |
+R |
+R |
R |
R |
M |
@@ -774,12 +774,42 @@ Longest: 24
TRUE |
-| 2010-08-20 |
-F1 |
+2012-11-28 |
+Y4 |
+Hospital A |
+B_ESCHR_COLI |
+S |
+S |
+R |
+R |
+F |
+Gram-negative |
+Escherichia |
+coli |
+TRUE |
+
+
+| 2010-08-07 |
+F10 |
Hospital B |
B_STRPT_PNMN |
-I |
-I |
+S |
+S |
+S |
+R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2017-09-28 |
+A7 |
+Hospital C |
+B_STRPT_PNMN |
+R |
+R |
S |
R |
M |
@@ -789,24 +819,9 @@ Longest: 24
TRUE |
-| 2016-05-20 |
-X2 |
-Hospital A |
-B_STPHY_AURS |
-R |
-I |
-S |
-R |
-F |
-Gram-positive |
-Staphylococcus |
-aureus |
-TRUE |
-
-
-| 2017-02-25 |
-Y7 |
-Hospital A |
+2010-05-24 |
+W9 |
+Hospital B |
B_STRPT_PNMN |
S |
S |
@@ -818,21 +833,6 @@ Longest: 24
pneumoniae |
TRUE |
-
-| 2016-01-31 |
-Y4 |
-Hospital C |
-B_ESCHR_COLI |
-S |
-S |
-S |
-R |
-F |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the bug_drug_combinations() function:
@@ -854,50 +854,50 @@ Longest: 24
| E. coli |
AMX |
-2244 |
-103 |
-2308 |
-4655 |
+2239 |
+144 |
+2283 |
+4666 |
| E. coli |
AMC |
-3412 |
-156 |
-1087 |
-4655 |
+3411 |
+155 |
+1100 |
+4666 |
| E. coli |
CIP |
-3414 |
+3389 |
0 |
-1241 |
-4655 |
+1277 |
+4666 |
| E. coli |
GEN |
-4073 |
+4077 |
0 |
-582 |
-4655 |
+589 |
+4666 |
| K. pneumoniae |
AMX |
0 |
0 |
-1183 |
-1183 |
+1176 |
+1176 |
| K. pneumoniae |
AMC |
-960 |
-38 |
-185 |
-1183 |
+910 |
+50 |
+216 |
+1176 |
@@ -920,34 +920,34 @@ Longest: 24
| E. coli |
GEN |
-4073 |
+4077 |
0 |
-582 |
-4655 |
+589 |
+4666 |
| K. pneumoniae |
GEN |
-1070 |
+1045 |
0 |
-113 |
-1183 |
+131 |
+1176 |
| S. aureus |
GEN |
-2442 |
+2422 |
0 |
-329 |
-2771 |
+295 |
+2717 |
| S. pneumoniae |
GEN |
0 |
0 |
-2156 |
-2156 |
+2101 |
+2101 |
@@ -961,7 +961,7 @@ Longest: 24
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:
+# [1] 0.5409006
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 |
-0.5467334 |
+0.5371953 |
| Hospital B |
-0.5472356 |
+0.5490456 |
| Hospital C |
-0.5282083 |
+0.5335844 |
| Hospital D |
-0.5523125 |
+0.5374532 |
@@ -1008,23 +1008,23 @@ Longest: 24
| Hospital A |
-0.5467334 |
-3199 |
+0.5371953 |
+3159 |
| Hospital B |
-0.5472356 |
-3726 |
+0.5490456 |
+3772 |
| Hospital C |
-0.5282083 |
-1613 |
+0.5335844 |
+1593 |
| Hospital D |
-0.5523125 |
-2227 |
+0.5374532 |
+2136 |
@@ -1047,27 +1047,27 @@ Longest: 24
| Escherichia |
-0.7664876 |
-0.8749731 |
-0.9735768 |
+0.7642520 |
+0.8737677 |
+0.9747107 |
| Klebsiella |
-0.8436179 |
-0.9044801 |
-0.9873204 |
+0.8163265 |
+0.8886054 |
+0.9855442 |
| Staphylococcus |
-0.7971851 |
-0.8812703 |
-0.9765428 |
+0.7935223 |
+0.8914244 |
+0.9775488 |
| Streptococcus |
-0.5343228 |
+0.5316516 |
0.0000000 |
-0.5343228 |
+0.5316516 |
@@ -1092,23 +1092,23 @@ Longest: 24
| Hospital A |
-54.7% |
-27.4% |
+53.7% |
+27.5% |
| Hospital B |
-54.7% |
-26.0% |
+54.9% |
+27.3% |
| Hospital C |
-52.8% |
-24.9% |
+53.4% |
+26.0% |
| Hospital D |
-55.2% |
-26.5% |
+53.7% |
+25.7% |
@@ -1206,17 +1206,17 @@ Longest: 24
mic_values <- random_mic(size = 100)
mic_values
# Class <mic>
-# [1] 32 <=0.001 0.025 <=0.001 4 0.125 0.01 0.002 32
-# [10] 16 64 4 <=0.001 0.01 16 0.01 64 64
-# [19] 256 0.0625 0.002 0.005 0.125 0.025 32 128 0.5
-# [28] 16 0.5 32 0.005 32 0.01 2 0.125 128
-# [37] 64 8 0.002 0.01 2 <=0.001 0.005 64 0.0625
-# [46] <=0.001 8 0.5 64 32 0.5 0.005 0.01 <=0.001
-# [55] 16 0.5 8 0.0625 0.125 128 16 0.5 0.002
-# [64] 16 8 128 128 4 256 0.5 8 4
-# [73] 16 0.025 2 1 16 0.005 0.01 16 1
-# [82] 0.25 0.01 0.002 0.0625 0.005 128 64 128 8
-# [91] 0.002 1 8 8 0.25 0.125 16 2 0.5
+# [1] 64 4 0.25 64 256 4 128 0.125 64
+# [10] 64 4 4 8 16 32 2 0.005 0.002
+# [19] 4 256 0.25 0.5 2 <=0.001 0.025 0.0625 32
+# [28] 1 128 0.005 0.0625 0.25 2 0.002 8 1
+# [37] 16 0.125 8 1 32 16 1 16 8
+# [46] 16 0.005 0.5 128 <=0.001 32 2 0.0625 0.5
+# [55] 2 64 128 4 0.5 16 0.0625 0.0625 0.002
+# [64] 0.25 0.025 4 16 32 0.0625 0.0625 0.5 0.5
+# [73] 0.002 32 16 0.005 1 0.25 256 0.25 0.025
+# [82] 128 8 0.25 0.0625 1 256 16 0.5 0.125
+# [91] 0.005 2 0.002 128 0.5 32 0.0625 0.025 0.125
# [100] 256
# base R:
@@ -1244,10 +1244,10 @@ Longest: 24
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
# Class <disk>
-# [1] 29 31 21 24 20 24 29 22 21 20 19 25 17 30 30 28 25 27 23 20 18 22 31 25 24
-# [26] 29 25 21 29 20 22 23 27 30 23 22 30 22 18 20 23 27 25 23 21 21 24 21 29 26
-# [51] 21 26 26 24 30 24 30 25 23 30 20 29 22 17 20 18 21 22 27 29 30 30 30 21 30
-# [76] 26 19 28 26 22 25 19 21 23 29 17 23 23 24 26 28 17 17 30 23 29 31 19 19 31
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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