Introduction
@@ -201,21 +201,21 @@
-| 2022-10-06 |
+2022-10-10 |
abcd |
Escherichia coli |
S |
S |
-| 2022-10-06 |
+2022-10-10 |
abcd |
Escherichia coli |
S |
R |
-| 2022-10-06 |
+2022-10-10 |
efgh |
Escherichia coli |
R |
@@ -325,70 +325,70 @@
-| 2017-11-17 |
-Y8 |
-Hospital B |
+2017-08-15 |
+V8 |
+Hospital C |
Streptococcus pneumoniae |
-I |
R |
R |
S |
+S |
F |
-| 2015-02-26 |
-V8 |
-Hospital D |
-Staphylococcus aureus |
-R |
+2013-01-31 |
+L3 |
+Hospital B |
+Escherichia coli |
S |
S |
S |
+S |
+M |
+
+
+| 2012-03-22 |
+Y6 |
+Hospital D |
+Escherichia coli |
+S |
+I |
+S |
+S |
F |
-
-| 2011-11-24 |
-I6 |
-Hospital D |
-Klebsiella pneumoniae |
+
+| 2012-02-11 |
+I1 |
+Hospital C |
+Staphylococcus aureus |
R |
S |
S |
S |
M |
-
-| 2013-06-23 |
-O2 |
-Hospital B |
-Escherichia coli |
-S |
-R |
-S |
-S |
-F |
-
-| 2010-10-16 |
-X2 |
-Hospital B |
-Escherichia coli |
-I |
-I |
-S |
-S |
-F |
-
-
-| 2012-03-22 |
-U10 |
+2012-09-29 |
+F5 |
Hospital A |
Escherichia coli |
-R |
-I |
+S |
+S |
+S |
+S |
+M |
+
+
+| 2017-03-01 |
+H10 |
+Hospital B |
+Staphylococcus aureus |
+S |
+S |
R |
S |
-F |
+M |
@@ -422,16 +422,16 @@ Longest: 1
| 1 |
M |
-10,375 |
-51.88% |
-10,375 |
-51.88% |
+10,361 |
+51.81% |
+10,361 |
+51.81% |
| 2 |
F |
-9,625 |
-48.13% |
+9,639 |
+48.20% |
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 10,694 'phenotype-based' first isolates (53.5% of total where a
+
# => Found 10,672 'phenotype-based' first isolates (53.4% of total where a
# microbial ID was available)
-So only 53.5% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:
+So only 53.4% 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 10,694 isolates for analysis. Now our data looks like:
+So we end up with 10,672 isolates for analysis. Now our data looks like:
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
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 %>%
@@ -975,19 +975,19 @@ Longest: 24
| Hospital A |
-0.5417823 |
+0.5367144 |
| Hospital B |
-0.5486465 |
+0.5420436 |
| Hospital C |
-0.5634971 |
+0.5339252 |
| Hospital D |
-0.5485369 |
+0.5478097 |
@@ -1008,23 +1008,23 @@ Longest: 24
| Hospital A |
-0.5417823 |
-3243 |
+0.5367144 |
+3214 |
| Hospital B |
-0.5486465 |
-3731 |
+0.5420436 |
+3758 |
| Hospital C |
-0.5634971 |
-1567 |
+0.5339252 |
+1577 |
| Hospital D |
-0.5485369 |
-2153 |
+0.5478097 |
+2123 |
@@ -1047,27 +1047,27 @@ Longest: 24
| Escherichia |
-0.7708831 |
-0.8791495 |
-0.9791712 |
+0.7743382 |
+0.8695559 |
+0.9739539 |
| Klebsiella |
-0.8193604 |
-0.9109767 |
-0.9783924 |
+0.8305384 |
+0.8905560 |
+0.9841130 |
| Staphylococcus |
-0.7871953 |
-0.8795926 |
-0.9770826 |
+0.7853782 |
+0.8910604 |
+0.9768368 |
| Streptococcus |
-0.5268472 |
+0.5363289 |
0.0000000 |
-0.5268472 |
+0.5363289 |
@@ -1092,22 +1092,22 @@ Longest: 24
| Hospital A |
-54.2% |
-26.2% |
+53.7% |
+26.5% |
| Hospital B |
-54.9% |
-27.0% |
+54.2% |
+26.3% |
| Hospital C |
-56.3% |
-28.1% |
+53.4% |
+25.1% |
| Hospital D |
-54.9% |
+54.8% |
27.1% |
@@ -1206,16 +1206,16 @@ Longest: 24
mic_values <- random_mic(size = 100)
mic_values
# Class <mic>
-# [1] 2 0.0625 0.25 128 64 256 0.01 0.01 0.0625 0.5
-# [11] 0.002 0.001 0.125 0.025 128 0.002 0.01 256 1 1
-# [21] 0.025 32 0.125 1 0.0625 1 2 1 0.25 32
-# [31] 0.0625 0.5 0.002 0.25 0.001 0.002 0.025 0.01 32 0.5
-# [41] 128 16 16 0.0625 4 256 256 16 64 0.125
-# [51] 0.01 0.01 8 0.01 2 256 64 1 0.5 32
-# [61] 0.025 2 16 0.005 0.025 16 2 64 8 4
-# [71] 16 0.5 0.01 16 8 0.0625 0.01 128 128 0.005
-# [81] 64 0.25 0.25 0.001 0.001 256 8 0.0625 0.125 0.01
-# [91] 0.5 8 64 0.5 0.002 0.002 32 128 4 128