Introduction
@@ -231,21 +231,21 @@ make the structure of your data generally look like this:
-| 2022-11-07 |
+2022-11-10 |
abcd |
Escherichia coli |
S |
S |
-| 2022-11-07 |
+2022-11-10 |
abcd |
Escherichia coli |
S |
R |
-| 2022-11-07 |
+2022-11-10 |
efgh |
Escherichia coli |
R |
@@ -395,31 +395,20 @@ data set:
-| 2015-05-10 |
-P6 |
+2014-05-09 |
+P10 |
Hospital B |
Klebsiella pneumoniae |
S |
S |
S |
-R |
+S |
F |
-| 2016-06-01 |
-N5 |
-Hospital B |
-Escherichia coli |
-R |
-S |
-R |
-S |
-M |
-
-
-| 2016-09-10 |
-H3 |
-Hospital C |
+2012-12-23 |
+H10 |
+Hospital D |
Streptococcus pneumoniae |
S |
R |
@@ -427,22 +416,33 @@ data set:
S |
M |
-
-| 2016-04-25 |
-K7 |
-Hospital B |
+
+| 2011-01-22 |
+L6 |
+Hospital A |
Escherichia coli |
R |
S |
-R |
+S |
+S |
+M |
+
+
+| 2013-03-14 |
+C1 |
+Hospital B |
+Escherichia coli |
+I |
+S |
+S |
S |
M |
-| 2016-10-17 |
-I6 |
-Hospital B |
-Escherichia coli |
+2012-07-02 |
+K8 |
+Hospital D |
+Streptococcus pneumoniae |
R |
S |
S |
@@ -450,11 +450,11 @@ data set:
M |
-| 2017-10-02 |
-S7 |
-Hospital C |
-Escherichia coli |
-I |
+2011-02-12 |
+U4 |
+Hospital B |
+Staphylococcus aureus |
+S |
S |
S |
S |
@@ -494,16 +494,16 @@ Longest: 1
| 1 |
M |
-10,394 |
-51.97% |
-10,394 |
-51.97% |
+10,478 |
+52.39% |
+10,478 |
+52.39% |
| 2 |
F |
-9,606 |
-48.03% |
+9,522 |
+47.61% |
20,000 |
100.00% |
@@ -616,7 +616,7 @@ 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 10,650 'phenotype-based' first isolates (53.3% of total where a
+# => Found 10,664 'phenotype-based' first isolates (53.3% of total where a
# microbial ID was available)
So only 53.3% is suitable for resistance analysis! We can now filter
on it with the filter() function, also from the
@@ -629,7 +629,7 @@ on it with the data_1st <- data %>%
filter_first_isolate()
# Including isolates from ICU.
-
So we end up with 10,650 isolates for analysis. Now our data looks
+
So we end up with 10,664 isolates for analysis. Now our data looks
like:
@@ -668,42 +668,10 @@ like:
-| 1 |
-2015-05-10 |
-P6 |
-Hospital B |
-B_KLBSL_PNMN |
-R |
-S |
-S |
-R |
-F |
-Gram-negative |
-Klebsiella |
-pneumoniae |
-TRUE |
-
-
-| 2 |
-2016-06-01 |
-N5 |
-Hospital B |
-B_ESCHR_COLI |
-R |
-S |
-R |
-S |
-M |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
-| 3 |
-2016-09-10 |
-H3 |
-Hospital C |
+5 |
+2012-07-02 |
+K8 |
+Hospital D |
B_STRPT_PNMN |
R |
R |
@@ -716,30 +684,14 @@ like:
TRUE |
-| 5 |
-2016-10-17 |
-I6 |
-Hospital B |
-B_ESCHR_COLI |
-R |
-S |
-S |
-S |
-M |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
| 8 |
-2012-01-16 |
-M3 |
-Hospital D |
+2012-03-12 |
+K1 |
+Hospital B |
B_STPHY_AURS |
-R |
-R |
-R |
+S |
+S |
+S |
S |
M |
Gram-positive |
@@ -747,17 +699,65 @@ like:
aureus |
TRUE |
-
-| 10 |
-2010-08-25 |
+
+| 9 |
+2012-02-20 |
U3 |
-Hospital C |
-B_STRPT_PNMN |
-R |
-R |
+Hospital B |
+B_ESCHR_COLI |
+S |
+S |
S |
R |
F |
+Gram-negative |
+Escherichia |
+coli |
+TRUE |
+
+
+| 10 |
+2016-05-10 |
+O8 |
+Hospital C |
+B_STRPT_PNMN |
+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 |
+TRUE |
+
+
+| 13 |
+2010-05-02 |
+L5 |
+Hospital D |
+B_STRPT_PNMN |
+S |
+S |
+S |
+R |
+M |
Gram-positive |
Streptococcus |
pneumoniae |
@@ -796,8 +796,8 @@ readable:
data_1st %>% freq(genus, species)
Frequency table
Class: character
-Length: 10,650
-Available: 10,650 (100%, NA: 0 = 0%)
+Length: 10,664
+Available: 10,664 (100%, NA: 0 = 0%)
Unique: 4
Shortest: 16
Longest: 24
@@ -822,33 +822,33 @@ Longest: 24
| 1 |
Escherichia coli |
-4,676 |
-43.91% |
-4,676 |
-43.91% |
+4,611 |
+43.24% |
+4,611 |
+43.24% |
| 2 |
Staphylococcus aureus |
-2,721 |
-25.55% |
-7,397 |
-69.46% |
+2,676 |
+25.09% |
+7,287 |
+68.33% |
| 3 |
Streptococcus pneumoniae |
-2,087 |
-19.60% |
-9,484 |
-89.05% |
+2,152 |
+20.18% |
+9,439 |
+88.51% |
| 4 |
Klebsiella pneumoniae |
-1,166 |
-10.95% |
-10,650 |
+1,225 |
+11.49% |
+10,664 |
100.00% |
@@ -897,24 +897,9 @@ antibiotic class they are in:
-| 2015-05-10 |
-P6 |
-Hospital B |
-B_KLBSL_PNMN |
-R |
-S |
-S |
-R |
-F |
-Gram-negative |
-Klebsiella |
-pneumoniae |
-TRUE |
-
-
-| 2016-09-10 |
-H3 |
-Hospital C |
+2012-07-02 |
+K8 |
+Hospital D |
B_STRPT_PNMN |
R |
R |
@@ -926,39 +911,54 @@ antibiotic class they are in:
pneumoniae |
TRUE |
-
-| 2010-08-25 |
-U3 |
-Hospital C |
-B_STRPT_PNMN |
-R |
-R |
-S |
-R |
-F |
-Gram-positive |
-Streptococcus |
-pneumoniae |
-TRUE |
-
-| 2016-11-19 |
-M8 |
-Hospital A |
+2012-02-20 |
+U3 |
+Hospital B |
B_ESCHR_COLI |
S |
S |
S |
R |
-M |
+F |
Gram-negative |
Escherichia |
coli |
TRUE |
-| 2011-04-24 |
-H4 |
+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 |
@@ -972,13 +972,13 @@ antibiotic class they are in:
TRUE |
-| 2017-11-30 |
-Z6 |
-Hospital C |
+2017-10-31 |
+U5 |
+Hospital A |
B_STRPT_PNMN |
S |
S |
-S |
+R |
R |
F |
Gram-positive |
@@ -1009,50 +1009,50 @@ different bug/drug combinations, you can use the
| E. coli |
AMX |
-2239 |
-111 |
-2326 |
-4676 |
+2188 |
+122 |
+2301 |
+4611 |
| E. coli |
AMC |
-3433 |
-145 |
-1098 |
-4676 |
+3364 |
+162 |
+1085 |
+4611 |
| E. coli |
CIP |
-3431 |
+3385 |
0 |
-1245 |
-4676 |
+1226 |
+4611 |
| E. coli |
GEN |
-4066 |
+4060 |
0 |
-610 |
-4676 |
+551 |
+4611 |
| K. pneumoniae |
AMX |
0 |
0 |
-1166 |
-1166 |
+1225 |
+1225 |
| K. pneumoniae |
AMC |
-907 |
-49 |
-210 |
-1166 |
+916 |
+69 |
+240 |
+1225 |
@@ -1075,34 +1075,34 @@ different bug/drug combinations, you can use the
| E. coli |
GEN |
-4066 |
+4060 |
0 |
-610 |
-4676 |
+551 |
+4611 |
| K. pneumoniae |
GEN |
-1048 |
+1095 |
0 |
-118 |
-1166 |
+130 |
+1225 |
| S. aureus |
GEN |
-2385 |
+2375 |
0 |
-336 |
-2721 |
+301 |
+2676 |
| S. pneumoniae |
GEN |
0 |
0 |
-2087 |
-2087 |
+2152 |
+2152 |
@@ -1134,7 +1134,7 @@ I (
proportion_SI(), equa
own:
+
# [1] 0.5425731
@@ -1149,19 +1149,19 @@ own:
| Hospital A |
-0.5551767 |
+0.5365469 |
| Hospital B |
-0.5362818 |
+0.5426068 |
| Hospital C |
-0.5477707 |
+0.5511222 |
| Hospital D |
-0.5404235 |
+0.5450684 |
@@ -1186,23 +1186,23 @@ all isolates available for every group (i.e. values S, I or R):
| Hospital A |
-0.5551767 |
-3226 |
+0.5365469 |
+3174 |
| Hospital B |
-0.5362818 |
-3776 |
+0.5426068 |
+3767 |
| Hospital C |
-0.5477707 |
-1570 |
+0.5511222 |
+1604 |
| Hospital D |
-0.5404235 |
-2078 |
+0.5450684 |
+2119 |
@@ -1227,27 +1227,27 @@ therapies very easily:
| Escherichia |
-0.7651839 |
-0.8695466 |
-0.9773311 |
+0.7646931 |
+0.8805031 |
+0.9750596 |
| Klebsiella |
-0.8198971 |
-0.8987993 |
-0.9785592 |
+0.8040816 |
+0.8938776 |
+0.9779592 |
| Staphylococcus |
-0.7897832 |
-0.8765160 |
-0.9816244 |
+0.7997010 |
+0.8875187 |
+0.9824365 |
| Streptococcus |
-0.5433637 |
+0.5473978 |
0.0000000 |
-0.5433637 |
+0.5473978 |
@@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
| Hospital A |
-55.5% |
-26.2% |
-
-
-| Hospital B |
-53.6% |
-26.6% |
-
-
-| Hospital C |
-54.8% |
+53.7% |
25.7% |
+| Hospital B |
+54.3% |
+27.0% |
+
+
+| Hospital C |
+55.1% |
+27.6% |
+
+
| Hospital D |
-54.0% |
-27.8% |
+54.5% |
+26.4% |
@@ -1407,16 +1407,18 @@ classes) <mic> and <disk>:
mic_values <- random_mic(size = 100)
mic_values
# Class 'mic'
-# [1] 16 64 0.0625 4 0.025 256 0.005 128 64 0.5
-# [11] 1 64 0.25 4 0.5 0.25 0.25 0.25 4 0.002
-# [21] 256 1 0.125 64 0.01 1 0.002 0.002 32 0.005
-# [31] 4 0.025 128 0.01 0.0625 0.25 0.0625 0.125 2 0.125
-# [41] 0.005 8 0.005 8 4 0.025 128 0.25 16 1
-# [51] 0.005 16 0.005 0.002 1 0.125 0.125 128 0.0625 0.125
-# [61] 0.025 0.002 256 0.01 0.25 0.002 0.002 0.002 0.005 256
-# [71] 0.0625 0.125 0.25 0.001 0.0625 4 0.025 64 0.01 8
-# [81] 0.25 32 0.005 0.005 0.001 128 128 8 256 0.0625
-# [91] 0.005 64 0.5 0.005 2 1 0.01 4 0.5 8