Introduction
@@ -231,21 +231,21 @@ make the structure of your data generally look like this:
-| 2022-11-10 |
+2022-11-12 |
abcd |
Escherichia coli |
S |
S |
-| 2022-11-10 |
+2022-11-12 |
abcd |
Escherichia coli |
S |
R |
-| 2022-11-10 |
+2022-11-12 |
efgh |
Escherichia coli |
R |
@@ -375,12 +375,12 @@ data set:
-
+
-
+
-| 2014-05-09 |
-P10 |
-Hospital B |
-Klebsiella pneumoniae |
-S |
-S |
-S |
-S |
-F |
-
-
-| 2012-12-23 |
-H10 |
-Hospital D |
-Streptococcus pneumoniae |
-S |
-R |
-S |
-S |
-M |
-
-
-| 2011-01-22 |
-L6 |
+2017-08-16 |
+S1 |
Hospital A |
Escherichia coli |
R |
S |
S |
-S |
-M |
+R |
+F |
-| 2013-03-14 |
-C1 |
+2014-12-04 |
+J1 |
Hospital B |
Escherichia coli |
-I |
-S |
-S |
-S |
-M |
-
-
-| 2012-07-02 |
-K8 |
-Hospital D |
-Streptococcus pneumoniae |
R |
S |
S |
S |
M |
+
+| 2012-07-21 |
+R6 |
+Hospital C |
+Escherichia coli |
+S |
+S |
+R |
+S |
+F |
+
-| 2011-02-12 |
-U4 |
-Hospital B |
+2012-11-26 |
+K8 |
+Hospital A |
Staphylococcus aureus |
S |
+R |
+S |
+S |
+M |
+
+
+| 2011-07-23 |
+Z2 |
+Hospital B |
+Escherichia coli |
+R |
+R |
+S |
+S |
+F |
+
+
+| 2016-05-31 |
+S7 |
+Hospital B |
+Escherichia coli |
+S |
S |
S |
S |
@@ -494,16 +494,16 @@ Longest: 1
| 1 |
M |
-10,478 |
-52.39% |
-10,478 |
-52.39% |
+10,563 |
+52.82% |
+10,563 |
+52.82% |
| 2 |
F |
-9,522 |
-47.61% |
+9,437 |
+47.19% |
20,000 |
100.00% |
@@ -616,9 +616,9 @@ takes into account the antimicrobial susceptibility test results using
# Basing inclusion on all antimicrobial results, using a points threshold of
# 2
# Including isolates from ICU.
-# => Found 10,664 'phenotype-based' first isolates (53.3% of total where a
+# => Found 10,633 'phenotype-based' first isolates (53.2% of total where a
# microbial ID was available)
-So only 53.3% is suitable for resistance analysis! We can now filter
+
So only 53.2% 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 10,664 isolates for analysis. Now our data looks
+
So we end up with 10,633 isolates for analysis. Now our data looks
like:
-
+
@@ -647,7 +647,7 @@ like:
-
+
-| 5 |
-2012-07-02 |
-K8 |
-Hospital D |
-B_STRPT_PNMN |
-R |
-R |
+3 |
+2012-07-21 |
+R6 |
+Hospital C |
+B_ESCHR_COLI |
+S |
S |
R |
-M |
-Gram-positive |
-Streptococcus |
-pneumoniae |
+S |
+F |
+Gram-negative |
+Escherichia |
+coli |
TRUE |
-| 8 |
-2012-03-12 |
-K1 |
-Hospital B |
+4 |
+2012-11-26 |
+K8 |
+Hospital A |
B_STPHY_AURS |
-S |
-S |
+R |
+R |
S |
S |
M |
@@ -700,15 +700,15 @@ like:
TRUE |
-| 9 |
-2012-02-20 |
-U3 |
+5 |
+2011-07-23 |
+Z2 |
Hospital B |
B_ESCHR_COLI |
-S |
-S |
-S |
R |
+R |
+S |
+S |
F |
Gram-negative |
Escherichia |
@@ -716,51 +716,51 @@ like:
TRUE |
-| 10 |
-2016-05-10 |
-O8 |
-Hospital C |
-B_STRPT_PNMN |
+6 |
+2016-05-31 |
+S7 |
+Hospital B |
+B_ESCHR_COLI |
S |
S |
S |
-R |
-F |
-Gram-positive |
-Streptococcus |
-pneumoniae |
-TRUE |
-
-
-| 11 |
-2015-12-30 |
-W3 |
-Hospital D |
-B_KLBSL_PNMN |
-R |
-S |
-S |
S |
F |
Gram-negative |
-Klebsiella |
-pneumoniae |
+Escherichia |
+coli |
+TRUE |
+
+
+| 7 |
+2011-07-29 |
+C9 |
+Hospital B |
+B_STPHY_AURS |
+R |
+S |
+S |
+S |
+M |
+Gram-positive |
+Staphylococcus |
+aureus |
TRUE |
-| 13 |
-2010-05-02 |
-L5 |
+14 |
+2016-07-22 |
+N8 |
Hospital D |
-B_STRPT_PNMN |
-S |
-S |
-S |
+B_ESCHR_COLI |
R |
-M |
-Gram-positive |
-Streptococcus |
-pneumoniae |
+R |
+S |
+S |
+F |
+Gram-negative |
+Escherichia |
+coli |
TRUE |
@@ -796,8 +796,8 @@ readable:
data_1st %>% freq(genus, species)
Frequency table
Class: character
-Length: 10,664
-Available: 10,664 (100%, NA: 0 = 0%)
+Length: 10,633
+Available: 10,633 (100%, NA: 0 = 0%)
Unique: 4
Shortest: 16
Longest: 24
@@ -822,33 +822,33 @@ Longest: 24
| 1 |
Escherichia coli |
-4,611 |
-43.24% |
-4,611 |
-43.24% |
+4,624 |
+43.49% |
+4,624 |
+43.49% |
| 2 |
Staphylococcus aureus |
-2,676 |
-25.09% |
-7,287 |
-68.33% |
+2,730 |
+25.67% |
+7,354 |
+69.16% |
| 3 |
Streptococcus pneumoniae |
-2,152 |
-20.18% |
-9,439 |
-88.51% |
+2,082 |
+19.58% |
+9,436 |
+88.74% |
| 4 |
Klebsiella pneumoniae |
-1,225 |
-11.49% |
-10,664 |
+1,197 |
+11.26% |
+10,633 |
100.00% |
@@ -897,83 +897,8 @@ antibiotic class they are in:
-| 2012-07-02 |
-K8 |
-Hospital D |
-B_STRPT_PNMN |
-R |
-R |
-S |
-R |
-M |
-Gram-positive |
-Streptococcus |
-pneumoniae |
-TRUE |
-
-
-| 2012-02-20 |
-U3 |
-Hospital B |
-B_ESCHR_COLI |
-S |
-S |
-S |
-R |
-F |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
-| 2016-05-10 |
-O8 |
-Hospital C |
-B_STRPT_PNMN |
-S |
-S |
-S |
-R |
-F |
-Gram-positive |
-Streptococcus |
-pneumoniae |
-TRUE |
-
-
-| 2010-05-02 |
-L5 |
-Hospital D |
-B_STRPT_PNMN |
-S |
-S |
-S |
-R |
-M |
-Gram-positive |
-Streptococcus |
-pneumoniae |
-TRUE |
-
-
-| 2012-09-16 |
-J7 |
-Hospital B |
-B_STRPT_PNMN |
-R |
-R |
-S |
-R |
-M |
-Gram-positive |
-Streptococcus |
-pneumoniae |
-TRUE |
-
-
-| 2017-10-31 |
-U5 |
+2012-12-19 |
+S3 |
Hospital A |
B_STRPT_PNMN |
S |
@@ -986,6 +911,81 @@ antibiotic class they are in:
pneumoniae |
TRUE |
+
+| 2013-04-29 |
+E8 |
+Hospital D |
+B_STRPT_PNMN |
+R |
+R |
+S |
+R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2014-11-08 |
+R2 |
+Hospital B |
+B_STRPT_PNMN |
+S |
+S |
+S |
+R |
+F |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2012-09-13 |
+W3 |
+Hospital B |
+B_STRPT_PNMN |
+S |
+S |
+R |
+R |
+F |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2017-11-23 |
+F9 |
+Hospital B |
+B_STRPT_PNMN |
+R |
+R |
+S |
+R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2014-07-26 |
+R5 |
+Hospital C |
+B_KLBSL_PNMN |
+R |
+S |
+S |
+R |
+F |
+Gram-negative |
+Klebsiella |
+pneumoniae |
+TRUE |
+
If you want to get a quick glance of the number of isolates in
@@ -1009,50 +1009,50 @@ different bug/drug combinations, you can use the
| E. coli |
AMX |
-2188 |
-122 |
-2301 |
-4611 |
+2175 |
+124 |
+2325 |
+4624 |
| E. coli |
AMC |
-3364 |
-162 |
-1085 |
-4611 |
+3402 |
+145 |
+1077 |
+4624 |
| E. coli |
CIP |
3385 |
0 |
-1226 |
-4611 |
+1239 |
+4624 |
| E. coli |
GEN |
-4060 |
+4046 |
0 |
-551 |
-4611 |
+578 |
+4624 |
| K. pneumoniae |
AMX |
0 |
0 |
-1225 |
-1225 |
+1197 |
+1197 |
| K. pneumoniae |
AMC |
-916 |
-69 |
-240 |
-1225 |
+922 |
+67 |
+208 |
+1197 |
@@ -1075,34 +1075,34 @@ different bug/drug combinations, you can use the
| E. coli |
GEN |
-4060 |
+4046 |
0 |
-551 |
-4611 |
+578 |
+4624 |
| K. pneumoniae |
GEN |
-1095 |
+1060 |
0 |
-130 |
-1225 |
+137 |
+1197 |
| S. aureus |
GEN |
-2375 |
+2411 |
0 |
-301 |
-2676 |
+319 |
+2730 |
| S. pneumoniae |
GEN |
0 |
0 |
-2152 |
-2152 |
+2082 |
+2082 |
@@ -1134,7 +1134,7 @@ I (
proportion_SI(), equa
own:
+
# [1] 0.5444371
@@ -1149,19 +1149,19 @@ own:
| Hospital A |
-0.5365469 |
+0.5425466 |
| Hospital B |
-0.5426068 |
+0.5360493 |
| Hospital C |
-0.5511222 |
+0.5492327 |
| Hospital D |
-0.5450684 |
+0.5585458 |
@@ -1186,23 +1186,23 @@ all isolates available for every group (i.e. values S, I or R):
| Hospital A |
-0.5365469 |
-3174 |
+0.5425466 |
+3220 |
| Hospital B |
-0.5426068 |
-3767 |
+0.5360493 |
+3731 |
| Hospital C |
-0.5511222 |
-1604 |
+0.5492327 |
+1564 |
| Hospital D |
-0.5450684 |
-2119 |
+0.5585458 |
+2118 |
@@ -1227,27 +1227,27 @@ therapies very easily:
| Escherichia |
-0.7646931 |
-0.8805031 |
-0.9750596 |
+0.7670848 |
+0.8750000 |
+0.9764273 |
| Klebsiella |
-0.8040816 |
-0.8938776 |
-0.9779592 |
+0.8262322 |
+0.8855472 |
+0.9791145 |
| Staphylococcus |
-0.7997010 |
-0.8875187 |
-0.9824365 |
+0.7908425 |
+0.8831502 |
+0.9754579 |
| Streptococcus |
-0.5473978 |
+0.5317003 |
0.0000000 |
-0.5473978 |
+0.5317003 |
@@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
| Hospital A |
-53.7% |
-25.7% |
+54.3% |
+25.2% |
| Hospital B |
-54.3% |
-27.0% |
+53.6% |
+26.7% |
| Hospital C |
-55.1% |
-27.6% |
+54.9% |
+25.9% |
| Hospital D |
-54.5% |
-26.4% |
+55.9% |
+29.3% |
@@ -1407,18 +1407,16 @@ classes) <mic> and <disk>:
mic_values <- random_mic(size = 100)
mic_values
# Class 'mic'
-# [1] 2 <=0.001 4 8 16 0.5 >=256 0.002 2
-# [10] 0.0625 <=0.001 0.025 0.002 0.002 0.005 0.5 32 2
-# [19] 4 0.0625 0.5 0.125 32 8 >=256 <=0.001 0.0625
-# [28] 1 0.025 0.01 0.25 64 4 4 0.01 0.002
-# [37] 0.025 0.25 128 8 2 0.005 64 1 >=256
-# [46] 0.002 0.25 0.25 16 0.005 0.0625 64 128 1
-# [55] 0.002 2 8 >=256 0.5 8 0.005 4 32
-# [64] 0.025 0.25 4 2 4 0.125 0.025 32 0.005
-# [73] 8 0.25 >=256 4 128 1 8 64 2
-# [82] 64 128 8 0.5 0.0625 0.025 0.01 0.01 64
-# [91] 1 0.01 8 32 1 2 64 0.0625 0.125
-# [100] 64