Introduction
@@ -236,21 +236,21 @@ make the structure of your data generally look like this:
-| 2022-11-24 |
+2022-11-28 |
abcd |
Escherichia coli |
S |
S |
-| 2022-11-24 |
+2022-11-28 |
abcd |
Escherichia coli |
S |
R |
-| 2022-11-24 |
+2022-11-28 |
efgh |
Escherichia coli |
R |
@@ -400,67 +400,67 @@ data set:
-| 2015-01-29 |
-L10 |
+2016-12-09 |
+B5 |
Hospital A |
-Escherichia coli |
+Klebsiella pneumoniae |
+I |
S |
R |
S |
+M |
+
+
+| 2013-12-22 |
+V7 |
+Hospital B |
+Escherichia coli |
+S |
+S |
+S |
+S |
+F |
+
+
+| 2011-09-01 |
+J7 |
+Hospital B |
+Streptococcus pneumoniae |
+R |
+S |
+S |
S |
M |
-| 2011-01-24 |
-S8 |
-Hospital B |
+2010-09-10 |
+N5 |
+Hospital A |
Escherichia coli |
-I |
S |
-R |
-R |
-F |
+S |
+S |
+S |
+M |
-| 2011-06-11 |
-U8 |
-Hospital D |
-Escherichia coli |
+2015-12-02 |
+E9 |
+Hospital B |
+Staphylococcus aureus |
S |
S |
R |
S |
-F |
+M |
-| 2013-08-22 |
-V5 |
-Hospital C |
-Escherichia coli |
-S |
-S |
-S |
-S |
-F |
-
-
-| 2017-05-12 |
-V3 |
+2012-01-20 |
+V9 |
Hospital B |
-Escherichia coli |
+Staphylococcus aureus |
S |
-S |
-S |
-S |
-F |
-
-
-| 2017-05-16 |
-X8 |
-Hospital C |
-Streptococcus pneumoniae |
-S |
-I |
+R |
S |
S |
F |
@@ -499,16 +499,16 @@ Longest: 1
| 1 |
M |
-10,350 |
-51.75% |
-10,350 |
-51.75% |
+10,502 |
+52.51% |
+10,502 |
+52.51% |
| 2 |
F |
-9,650 |
-48.25% |
+9,498 |
+47.49% |
20,000 |
100.00% |
@@ -621,9 +621,9 @@ 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 10,691 'phenotype-based' first isolates (53.5% of total where a
+# => Found 10,638 'phenotype-based' first isolates (53.2% of total where a
# microbial ID was available)
-So only 53.5% 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 10,691 isolates for analysis. Now our data looks
+
So we end up with 10,638 isolates for analysis. Now our data looks
like:
-
@@ -651,12 +650,11 @@ like:
-
+
-| 1 |
-2015-01-29 |
-L10 |
+2016-12-09 |
+B5 |
+Hospital A |
+B_KLBSL_PNMN |
+R |
+S |
+R |
+S |
+M |
+Gram-negative |
+Klebsiella |
+pneumoniae |
+TRUE |
+
+
+| 2013-12-22 |
+V7 |
+Hospital B |
+B_ESCHR_COLI |
+S |
+S |
+S |
+S |
+F |
+Gram-negative |
+Escherichia |
+coli |
+TRUE |
+
+
+| 2011-09-01 |
+J7 |
+Hospital B |
+B_STRPT_PNMN |
+R |
+R |
+S |
+R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2010-09-10 |
+N5 |
Hospital A |
B_ESCHR_COLI |
-R |
-R |
+S |
+S |
S |
S |
M |
@@ -688,84 +730,34 @@ like:
coli |
TRUE |
-
-| 2 |
-2011-01-24 |
-S8 |
-Hospital B |
-B_ESCHR_COLI |
-I |
-S |
-R |
-R |
-F |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-| 3 |
-2011-06-11 |
-U8 |
-Hospital D |
-B_ESCHR_COLI |
+2015-12-02 |
+E9 |
+Hospital B |
+B_STPHY_AURS |
S |
S |
R |
S |
-F |
-Gram-negative |
-Escherichia |
-coli |
+M |
+Gram-positive |
+Staphylococcus |
+aureus |
TRUE |
-| 5 |
-2017-05-12 |
-V3 |
+2012-01-20 |
+V9 |
Hospital B |
-B_ESCHR_COLI |
-S |
-S |
-S |
-S |
-F |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
-| 6 |
-2017-05-16 |
-X8 |
-Hospital C |
-B_STRPT_PNMN |
-S |
-S |
-S |
+B_STPHY_AURS |
R |
+R |
+S |
+S |
F |
Gram-positive |
-Streptococcus |
-pneumoniae |
-TRUE |
-
-
-| 10 |
-2012-08-19 |
-N7 |
-Hospital B |
-B_ESCHR_COLI |
-S |
-S |
-R |
-S |
-F |
-Gram-negative |
-Escherichia |
-coli |
+Staphylococcus |
+aureus |
TRUE |
@@ -801,8 +793,8 @@ readable:
data_1st %>% freq(genus, species)
Frequency table
Class: character
-Length: 10,691
-Available: 10,691 (100%, NA: 0 = 0%)
+Length: 10,638
+Available: 10,638 (100%, NA: 0 = 0%)
Unique: 4
Shortest: 16
Longest: 24
@@ -827,33 +819,33 @@ Longest: 24
| 1 |
Escherichia coli |
-4,607 |
-43.09% |
-4,607 |
-43.09% |
+4,646 |
+43.67% |
+4,646 |
+43.67% |
| 2 |
Staphylococcus aureus |
-2,750 |
-25.72% |
-7,357 |
-68.81% |
+2,743 |
+25.78% |
+7,389 |
+69.46% |
| 3 |
Streptococcus pneumoniae |
-2,124 |
-19.87% |
-9,481 |
-88.68% |
+2,065 |
+19.41% |
+9,454 |
+88.87% |
| 4 |
Klebsiella pneumoniae |
-1,210 |
-11.32% |
-10,691 |
+1,184 |
+11.13% |
+10,638 |
100.00% |
@@ -874,14 +866,14 @@ antibiotic class they are in:
-
+
-
+
@@ -902,13 +894,43 @@ antibiotic class they are in:
-| 2011-01-24 |
-S8 |
+2011-09-01 |
+J7 |
Hospital B |
-B_ESCHR_COLI |
-I |
+B_STRPT_PNMN |
+R |
+R |
S |
R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2014-11-04 |
+C7 |
+Hospital C |
+B_STRPT_PNMN |
+R |
+R |
+S |
+R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2010-05-22 |
+X1 |
+Hospital C |
+B_ESCHR_COLI |
+R |
+I |
+S |
R |
F |
Gram-negative |
@@ -917,68 +939,38 @@ antibiotic class they are in:
TRUE |
-| 2017-05-16 |
-X8 |
+2011-03-20 |
+A1 |
Hospital C |
B_STRPT_PNMN |
-S |
-S |
+R |
+R |
S |
R |
-F |
+M |
Gram-positive |
Streptococcus |
pneumoniae |
TRUE |
-| 2011-11-29 |
-N9 |
-Hospital D |
-B_STPHY_AURS |
-S |
-S |
-S |
-R |
-F |
-Gram-positive |
-Staphylococcus |
-aureus |
-TRUE |
-
-
-| 2017-09-27 |
-I4 |
+2016-05-13 |
+K9 |
Hospital A |
-B_STPHY_AURS |
+B_STRPT_PNMN |
S |
S |
S |
R |
M |
Gram-positive |
-Staphylococcus |
-aureus |
-TRUE |
-
-
-| 2010-01-03 |
-N7 |
-Hospital B |
-B_STRPT_PNMN |
-R |
-R |
-S |
-R |
-F |
-Gram-positive |
Streptococcus |
pneumoniae |
TRUE |
-| 2011-05-07 |
-W8 |
+2014-01-21 |
+Q10 |
Hospital D |
B_STRPT_PNMN |
S |
@@ -1013,50 +1005,50 @@ different bug/drug combinations, you can use the
| E. coli |
AMX |
-2169 |
-130 |
-2308 |
-4607 |
+2171 |
+147 |
+2328 |
+4646 |
| E. coli |
AMC |
-3397 |
-171 |
-1039 |
-4607 |
+3429 |
+157 |
+1060 |
+4646 |
| E. coli |
CIP |
-3369 |
+3354 |
0 |
-1238 |
-4607 |
+1292 |
+4646 |
| E. coli |
GEN |
-4021 |
+4083 |
0 |
-586 |
-4607 |
+563 |
+4646 |
| K. pneumoniae |
AMX |
0 |
0 |
-1210 |
-1210 |
+1184 |
+1184 |
| K. pneumoniae |
AMC |
-941 |
-45 |
-224 |
-1210 |
+936 |
+42 |
+206 |
+1184 |
@@ -1078,34 +1070,34 @@ different bug/drug combinations, you can use the
| E. coli |
GEN |
-4021 |
+4083 |
0 |
-586 |
-4607 |
+563 |
+4646 |
| K. pneumoniae |
GEN |
-1081 |
+1073 |
0 |
-129 |
-1210 |
+111 |
+1184 |
| S. aureus |
GEN |
-2427 |
+2435 |
0 |
-323 |
-2750 |
+308 |
+2743 |
| S. pneumoniae |
GEN |
0 |
0 |
-2124 |
-2124 |
+2065 |
+2065 |
@@ -1137,7 +1129,7 @@ I (
proportion_SI(), equa
own:
+
# [1] 0.5455913
@@ -1152,19 +1144,19 @@ own:
| Hospital A |
-0.5395156 |
+0.5382918 |
| Hospital B |
-0.5511053 |
+0.5347408 |
| Hospital C |
-0.5408886 |
+0.5776965 |
| Hospital D |
-0.5535963 |
+0.5509126 |
@@ -1189,23 +1181,23 @@ all isolates available for every group (i.e. values S, I or R):
| Hospital A |
-0.5395156 |
-3138 |
+0.5382918 |
+3173 |
| Hospital B |
-0.5511053 |
-3845 |
+0.5347408 |
+3742 |
| Hospital C |
-0.5408886 |
-1553 |
+0.5776965 |
+1641 |
| Hospital D |
-0.5535963 |
-2155 |
+0.5509126 |
+2082 |
@@ -1230,27 +1222,27 @@ therapies very easily:
| Escherichia |
-0.7744736 |
-0.8728023 |
-0.9791621 |
+0.7718467 |
+0.8788205 |
+0.9750323 |
| Klebsiella |
-0.8148760 |
-0.8933884 |
-0.9809917 |
+0.8260135 |
+0.9062500 |
+0.9873311 |
| Staphylococcus |
-0.7949091 |
-0.8825455 |
-0.9800000 |
+0.7907401 |
+0.8877142 |
+0.9817718 |
| Streptococcus |
-0.5343691 |
+0.5438257 |
0.0000000 |
-0.5343691 |
+0.5438257 |
@@ -1278,23 +1270,23 @@ classes, use a antibiotic class selector such as
| Hospital A |
-54.0% |
-25.7% |
+53.8% |
+25.3% |
| Hospital B |
-55.1% |
-26.8% |
+53.5% |
+25.1% |
| Hospital C |
-54.1% |
-26.3% |
+57.8% |
+30.1% |
| Hospital D |
-55.4% |
-26.4% |
+55.1% |
+26.3% |
@@ -1410,16 +1402,18 @@ classes) <mic> and <disk>:
mic_values <- random_mic(size = 100)
mic_values
# Class 'mic'
-# [1] 128 0.002 4 64 64 0.125 1 256 32 0.001
-# [11] 32 0.5 1 4 0.25 8 4 0.005 16 256
-# [21] 16 16 128 0.125 0.125 16 0.25 4 0.005 2
-# [31] 0.25 1 2 0.01 0.5 256 8 0.025 0.125 0.125
-# [41] 8 0.5 8 0.5 0.25 1 0.001 256 1 64
-# [51] 0.01 0.001 1 0.25 0.125 32 4 16 8 0.001
-# [61] 256 0.025 16 0.01 0.25 64 64 128 0.25 1
-# [71] 0.025 256 0.001 0.5 0.001 64 0.5 64 32 0.025
-# [81] 0.125 0.002 0.005 2 8 256 16 8 16 0.002
-# [91] 128 0.0625 256 256 0.005 0.25 0.005 0.125 64 0.5