Introduction
@@ -236,21 +236,21 @@ make the structure of your data generally look like this:
-| 2023-01-05 |
+2023-01-06 |
abcd |
Escherichia coli |
S |
S |
-| 2023-01-05 |
+2023-01-06 |
abcd |
Escherichia coli |
S |
R |
-| 2023-01-05 |
+2023-01-06 |
efgh |
Escherichia coli |
R |
@@ -380,12 +380,12 @@ data set:
-
+
-
+
-| 2015-01-04 |
-C10 |
+2013-11-17 |
+D4 |
Hospital A |
-Escherichia coli |
-R |
-I |
+Streptococcus pneumoniae |
+S |
+S |
S |
S |
M |
-| 2010-08-21 |
-N3 |
+2014-12-24 |
+S2 |
Hospital B |
-Staphylococcus aureus |
-S |
-I |
+Streptococcus pneumoniae |
S |
S |
-M |
+S |
+S |
+F |
-| 2015-12-21 |
-Q3 |
-Hospital C |
-Staphylococcus aureus |
+2014-08-31 |
+Q4 |
+Hospital B |
+Escherichia coli |
+S |
S |
S |
S |
-R |
F |
-| 2015-10-03 |
-C5 |
+2012-08-04 |
+N10 |
+Hospital B |
+Streptococcus pneumoniae |
+S |
+S |
+S |
+S |
+F |
+
+
+| 2016-03-16 |
+D5 |
Hospital D |
Staphylococcus aureus |
-S |
-S |
+R |
+I |
S |
S |
M |
-
-| 2017-12-17 |
-O7 |
-Hospital B |
-Staphylococcus aureus |
-S |
-S |
-S |
-S |
-F |
-
-| 2014-08-04 |
+2016-10-07 |
O7 |
-Hospital B |
-Escherichia coli |
-R |
+Hospital D |
+Streptococcus pneumoniae |
+S |
S |
S |
S |
@@ -499,16 +499,16 @@ Longest: 1
| 1 |
M |
-10,374 |
-51.87% |
-10,374 |
-51.87% |
+10,466 |
+52.33% |
+10,466 |
+52.33% |
| 2 |
F |
-9,626 |
-48.13% |
+9,534 |
+47.67% |
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 10,551 'phenotype-based' first isolates (52.8% of total where a
+# => Found 10,633 'phenotype-based' first isolates (53.2% of total where a
# microbial ID was available)
-So only 52.8% 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 10,551 isolates for analysis. Now our data looks
+
So we end up with 10,633 isolates for analysis. Now our data looks
like:
@@ -673,77 +673,13 @@ like:
-| 4 |
-2015-10-03 |
-C5 |
-Hospital D |
-B_STPHY_AURS |
-S |
-S |
-S |
-S |
-M |
-Gram-positive |
-Staphylococcus |
-aureus |
-TRUE |
-
-
-| 6 |
-2014-08-04 |
-O7 |
-Hospital B |
-B_ESCHR_COLI |
-R |
-S |
-S |
-S |
-F |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
-| 8 |
-2017-05-16 |
-L1 |
-Hospital B |
-B_KLBSL_PNMN |
-R |
-S |
-S |
-S |
-M |
-Gram-negative |
-Klebsiella |
-pneumoniae |
-TRUE |
-
-
-| 9 |
-2016-05-28 |
-D3 |
-Hospital A |
-B_KLBSL_PNMN |
-R |
-S |
-S |
-S |
-M |
-Gram-negative |
-Klebsiella |
-pneumoniae |
-TRUE |
-
-
-| 10 |
-2011-02-19 |
-B7 |
+1 |
+2013-11-17 |
+D4 |
Hospital A |
B_STRPT_PNMN |
-R |
-R |
+S |
+S |
S |
R |
M |
@@ -753,14 +689,78 @@ like:
TRUE |
-| 11 |
-2014-12-17 |
-L4 |
+2 |
+2014-12-24 |
+S2 |
Hospital B |
+B_STRPT_PNMN |
+S |
+S |
+S |
+R |
+F |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 5 |
+2016-03-16 |
+D5 |
+Hospital D |
+B_STPHY_AURS |
+R |
+I |
+S |
+S |
+M |
+Gram-positive |
+Staphylococcus |
+aureus |
+TRUE |
+
+
+| 7 |
+2011-09-05 |
+Z1 |
+Hospital C |
+B_STPHY_AURS |
+S |
+S |
+R |
+S |
+F |
+Gram-positive |
+Staphylococcus |
+aureus |
+TRUE |
+
+
+| 8 |
+2015-09-14 |
+B4 |
+Hospital B |
+B_STRPT_PNMN |
+S |
+S |
+S |
+R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 9 |
+2013-09-14 |
+G4 |
+Hospital D |
B_ESCHR_COLI |
-R |
-R |
-R |
+S |
+S |
+S |
S |
M |
Gram-negative |
@@ -801,8 +801,8 @@ readable:
data_1st %>% freq(genus, species)
Frequency table
Class: character
-Length: 10,551
-Available: 10,551 (100%, NA: 0 = 0%)
+Length: 10,633
+Available: 10,633 (100%, NA: 0 = 0%)
Unique: 4
Shortest: 16
Longest: 24
@@ -827,33 +827,33 @@ Longest: 24
| 1 |
Escherichia coli |
-4,551 |
-43.13% |
-4,551 |
-43.13% |
+4,608 |
+43.34% |
+4,608 |
+43.34% |
| 2 |
Staphylococcus aureus |
-2,712 |
-25.70% |
-7,263 |
-68.84% |
+2,724 |
+25.62% |
+7,332 |
+68.96% |
| 3 |
Streptococcus pneumoniae |
-2,106 |
-19.96% |
-9,369 |
-88.80% |
+2,080 |
+19.56% |
+9,412 |
+88.52% |
| 4 |
Klebsiella pneumoniae |
-1,182 |
-11.20% |
-10,551 |
+1,221 |
+11.48% |
+10,633 |
100.00% |
@@ -874,14 +874,14 @@ antibiotic class they are in:
-
+
-
+
@@ -902,12 +902,12 @@ antibiotic class they are in:
-| 2011-02-19 |
-B7 |
+2013-11-17 |
+D4 |
Hospital A |
B_STRPT_PNMN |
-R |
-R |
+S |
+S |
S |
R |
M |
@@ -917,13 +917,13 @@ antibiotic class they are in:
TRUE |
-| 2013-06-20 |
-U2 |
+2014-12-24 |
+S2 |
Hospital B |
B_STRPT_PNMN |
S |
S |
-R |
+S |
R |
F |
Gram-positive |
@@ -932,27 +932,42 @@ antibiotic class they are in:
TRUE |
-| 2011-08-12 |
-V7 |
-Hospital D |
-B_STPHY_AURS |
+2015-09-14 |
+B4 |
+Hospital B |
+B_STRPT_PNMN |
+S |
+S |
+S |
+R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2011-02-25 |
+P4 |
+Hospital C |
+B_STRPT_PNMN |
R |
R |
S |
R |
F |
Gram-positive |
-Staphylococcus |
-aureus |
+Streptococcus |
+pneumoniae |
TRUE |
-
-| 2015-05-21 |
-I4 |
+
+| 2015-04-27 |
+C10 |
Hospital B |
B_STRPT_PNMN |
-R |
-R |
+S |
+S |
R |
R |
M |
@@ -961,31 +976,16 @@ antibiotic class they are in:
pneumoniae |
TRUE |
-
-| 2010-01-23 |
-F9 |
-Hospital B |
-B_ESCHR_COLI |
-S |
-S |
-R |
-R |
-M |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-| 2016-04-22 |
-Y4 |
-Hospital A |
+2011-03-11 |
+J4 |
+Hospital C |
B_STRPT_PNMN |
R |
R |
S |
R |
-F |
+M |
Gram-positive |
Streptococcus |
pneumoniae |
@@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
| E. coli |
AMX |
-2163 |
-127 |
-2261 |
-4551 |
+2140 |
+128 |
+2340 |
+4608 |
| E. coli |
AMC |
-3376 |
-131 |
-1044 |
-4551 |
+3336 |
+178 |
+1094 |
+4608 |
| E. coli |
CIP |
-3407 |
+3373 |
0 |
-1144 |
-4551 |
+1235 |
+4608 |
| E. coli |
GEN |
-4018 |
+4042 |
0 |
-533 |
-4551 |
+566 |
+4608 |
| K. pneumoniae |
AMX |
0 |
0 |
-1182 |
-1182 |
+1221 |
+1221 |
| K. pneumoniae |
AMC |
-920 |
-46 |
-216 |
-1182 |
+951 |
+51 |
+219 |
+1221 |
@@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
| E. coli |
GEN |
-4018 |
+4042 |
0 |
-533 |
-4551 |
+566 |
+4608 |
| K. pneumoniae |
GEN |
-1073 |
+1121 |
0 |
-109 |
-1182 |
+100 |
+1221 |
| S. aureus |
GEN |
-2408 |
+2432 |
0 |
-304 |
-2712 |
+292 |
+2724 |
| S. pneumoniae |
GEN |
0 |
0 |
-2106 |
-2106 |
+2080 |
+2080 |
@@ -1137,7 +1137,7 @@ I (
proportion_SI(), equa
own:
+
# [1] 0.5483871
@@ -1152,19 +1152,19 @@ own:
| Hospital A |
-0.5512346 |
+0.5436433 |
| Hospital B |
-0.5463693 |
+0.5441137 |
| Hospital C |
-0.5256817 |
+0.5588420 |
| Hospital D |
-0.5464268 |
+0.5550395 |
@@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):
| Hospital A |
-0.5512346 |
-3240 |
+0.5436433 |
+3162 |
| Hospital B |
-0.5463693 |
-3677 |
+0.5441137 |
+3729 |
| Hospital C |
-0.5256817 |
-1577 |
+0.5588420 |
+1589 |
| Hospital D |
-0.5464268 |
-2057 |
+0.5550395 |
+2153 |
@@ -1230,27 +1230,27 @@ therapies very easily:
| Escherichia |
-0.7705999 |
-0.8828829 |
-0.9817623 |
+0.7625868 |
+0.8771701 |
+0.9743924 |
| Klebsiella |
-0.8172589 |
-0.9077834 |
-0.9856176 |
+0.8206388 |
+0.9180999 |
+0.9844390 |
| Staphylococcus |
-0.7912979 |
-0.8879056 |
-0.9782448 |
+0.7830396 |
+0.8928047 |
+0.9805433 |
| Streptococcus |
-0.5251662 |
+0.5447115 |
0.0000000 |
-0.5251662 |
+0.5447115 |
@@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
| Hospital A |
-55.1% |
-27.0% |
+54.4% |
+25.9% |
| Hospital B |
-54.6% |
-27.7% |
+54.4% |
+27.1% |
| Hospital C |
-52.6% |
-24.6% |
+55.9% |
+28.1% |
| Hospital D |
-54.6% |
-26.5% |
+55.5% |
+26.6% |
@@ -1410,16 +1410,16 @@ classes) <mic> and <disk>:
mic_values <- random_mic(size = 100)
mic_values
# Class 'mic'
-# [1] 16 4 0.025 1 0.025 0.0625 0.125 2 0.001 >=256
-# [11] 4 0.025 128 >=256 128 4 0.0625 16 2 0.0625
-# [21] 128 64 0.25 0.5 0.002 2 128 4 0.002 0.025
-# [31] 128 0.0625 64 32 32 4 >=256 128 0.5 4
-# [41] 32 16 1 0.002 32 64 0.25 0.025 128 0.5
-# [51] 0.25 8 0.001 8 0.025 64 0.002 2 0.005 0.5
-# [61] 0.5 8 0.25 2 8 4 0.002 8 0.002 0.001
-# [71] 0.025 >=256 128 16 16 4 0.025 0.5 0.005 0.025
-# [81] 0.5 4 0.005 128 16 16 32 0.002 128 0.25
-# [91] 2 0.25 0.125 64 16 32 64 128 0.002 0.025