-| 2011-02-07 |
-G7 |
+2015-12-16 |
+B5 |
Hospital B |
-Escherichia coli |
+Streptococcus pneumoniae |
+R |
+R |
+I |
S |
+M |
+
+
+| 2017-01-08 |
+J1 |
+Hospital D |
+Streptococcus pneumoniae |
+R |
+R |
+I |
+R |
+M |
+
+
+| 2013-11-05 |
+N5 |
+Hospital D |
+Staphylococcus aureus |
+I |
S |
S |
R |
M |
-| 2016-04-30 |
-C8 |
-Hospital B |
+2010-12-18 |
+E4 |
+Hospital D |
Escherichia coli |
R |
-R |
+I |
R |
S |
M |
-| 2013-01-08 |
-R7 |
-Hospital C |
-Escherichia coli |
-S |
-S |
-I |
-S |
-F |
-
-
-| 2010-01-11 |
-Z6 |
+2012-09-14 |
+G1 |
Hospital A |
-Staphylococcus aureus |
-R |
-R |
-S |
-R |
-F |
-
-
-| 2017-06-16 |
-P4 |
-Hospital B |
Escherichia coli |
-I |
-I |
+R |
R |
S |
-F |
+R |
+M |
-| 2017-06-05 |
-C6 |
-Hospital C |
-Staphylococcus aureus |
-S |
+2011-09-02 |
+M4 |
+Hospital D |
+Escherichia coli |
I |
+R |
S |
S |
M |
@@ -510,16 +510,16 @@ Longest: 1
| 1 |
M |
-10,413 |
-52.07% |
-10,413 |
-52.07% |
+10,451 |
+52.26% |
+10,451 |
+52.26% |
| 2 |
F |
-9,587 |
-47.94% |
+9,549 |
+47.75% |
20,000 |
100.00% |
@@ -632,9 +632,9 @@ 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 12,241 'phenotype-based' first isolates (61.2% of total where a
+# => Found 12,299 'phenotype-based' first isolates (61.5% of total where a
# microbial ID was available)
-So only 61.2% is suitable for resistance analysis! We can now filter
+
So only 61.5% 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 12 241 isolates for analysis. Now our data looks
+
So we end up with 12 299 isolates for analysis. Now our data looks
like:
-
+
@@ -662,7 +662,7 @@ like:
-
+
| 1 |
-2011-02-07 |
-G7 |
+2015-12-16 |
+B5 |
Hospital B |
-B_ESCHR_COLI |
-S |
-S |
-S |
+B_STRPT_PNMN |
+R |
+R |
+I |
R |
M |
-Gram-negative |
-Escherichia |
-coli |
+Gram-positive |
+Streptococcus |
+pneumoniae |
TRUE |
| 2 |
-2016-04-30 |
-C8 |
-Hospital B |
-B_ESCHR_COLI |
+2017-01-08 |
+J1 |
+Hospital D |
+B_STRPT_PNMN |
R |
R |
+I |
R |
-S |
M |
-Gram-negative |
-Escherichia |
-coli |
+Gram-positive |
+Streptococcus |
+pneumoniae |
TRUE |
| 3 |
-2013-01-08 |
-R7 |
-Hospital C |
-B_ESCHR_COLI |
-S |
-S |
+2013-11-05 |
+N5 |
+Hospital D |
+B_STPHY_AURS |
I |
S |
-F |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
-| 4 |
-2010-01-11 |
-Z6 |
-Hospital A |
-B_STPHY_AURS |
-R |
-R |
S |
R |
-F |
+M |
Gram-positive |
Staphylococcus |
aureus |
TRUE |
+
+| 5 |
+2012-09-14 |
+G1 |
+Hospital A |
+B_ESCHR_COLI |
+R |
+R |
+S |
+R |
+M |
+Gram-negative |
+Escherichia |
+coli |
+TRUE |
+
-| 6 |
-2017-06-05 |
-C6 |
-Hospital C |
+7 |
+2016-07-29 |
+A6 |
+Hospital B |
B_STPHY_AURS |
S |
S |
-S |
+R |
S |
M |
Gram-positive |
@@ -763,19 +763,19 @@ like:
TRUE |
-| 7 |
-2015-07-18 |
-F7 |
-Hospital B |
-B_ESCHR_COLI |
-S |
-S |
+8 |
+2010-08-11 |
+J10 |
+Hospital C |
+B_KLBSL_PNMN |
R |
R |
+S |
+R |
M |
Gram-negative |
-Escherichia |
-coli |
+Klebsiella |
+pneumoniae |
TRUE |
@@ -811,8 +811,8 @@ readable:
data_1st %>% freq(genus, species)
Frequency table
Class: character
-Length: 12,241
-Available: 12,241 (100%, NA: 0 = 0%)
+Length: 12,299
+Available: 12,299 (100%, NA: 0 = 0%)
Unique: 4
Shortest: 16
Longest: 24
@@ -837,33 +837,33 @@ Longest: 24
| 1 |
Escherichia coli |
-5,831 |
-47.63% |
-5,831 |
-47.63% |
+5,862 |
+47.66% |
+5,862 |
+47.66% |
| 2 |
Staphylococcus aureus |
-3,241 |
-26.48% |
-9,072 |
-74.11% |
+3,231 |
+26.27% |
+9,093 |
+73.93% |
| 3 |
Streptococcus pneumoniae |
-1,857 |
-15.17% |
-10,929 |
-89.28% |
+1,864 |
+15.16% |
+10,957 |
+89.09% |
| 4 |
Klebsiella pneumoniae |
-1,312 |
-10.72% |
-12,241 |
+1,342 |
+10.91% |
+12,299 |
100.00% |
@@ -884,15 +884,15 @@ antibiotic class they are in:
-
-
-
-
-
+
+
+
+
+
+
-
-
+
-| 2011-02-07 |
-G7 |
+2015-12-16 |
+B5 |
Hospital B |
-B_ESCHR_COLI |
-S |
+B_STRPT_PNMN |
+R |
+R |
+I |
+R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2017-01-08 |
+J1 |
+Hospital D |
+B_STRPT_PNMN |
+R |
+R |
+I |
+R |
+M |
+Gram-positive |
+Streptococcus |
+pneumoniae |
+TRUE |
+
+
+| 2013-11-05 |
+N5 |
+Hospital D |
+B_STPHY_AURS |
+I |
S |
S |
R |
M |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
-| 2010-01-11 |
-Z6 |
-Hospital A |
-B_STPHY_AURS |
-R |
-R |
-S |
-R |
-F |
Gram-positive |
Staphylococcus |
aureus |
TRUE |
-
-| 2015-07-18 |
-F7 |
-Hospital B |
+
+| 2012-09-14 |
+G1 |
+Hospital A |
B_ESCHR_COLI |
-S |
-S |
R |
R |
+S |
+R |
M |
Gram-negative |
Escherichia |
coli |
TRUE |
-
-| 2017-10-11 |
-X3 |
-Hospital D |
-B_ESCHR_COLI |
-I |
+
+| 2010-08-11 |
+J10 |
+Hospital C |
+B_KLBSL_PNMN |
+R |
+R |
S |
R |
+M |
+Gram-negative |
+Klebsiella |
+pneumoniae |
+TRUE |
+
+
+| 2013-06-29 |
+S10 |
+Hospital A |
+B_STRPT_PNMN |
+R |
+R |
+R |
R |
F |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
-| 2015-05-07 |
-J3 |
-Hospital A |
-B_ESCHR_COLI |
-I |
-I |
-R |
-R |
-M |
-Gram-negative |
-Escherichia |
-coli |
-TRUE |
-
-
-| 2013-12-05 |
-D10 |
-Hospital B |
-B_ESCHR_COLI |
-R |
-R |
-R |
-R |
-M |
-Gram-negative |
-Escherichia |
-coli |
+Gram-positive |
+Streptococcus |
+pneumoniae |
TRUE |
@@ -1025,46 +1025,46 @@ different bug/drug combinations, you can use the
2 |
E. coli |
AMC |
-2728 |
-1160 |
-1943 |
-5831 |
+2700 |
+1233 |
+1929 |
+5862 |
| 1 |
E. coli |
AMX |
-1490 |
-1233 |
-3108 |
-5831 |
+1457 |
+1262 |
+3143 |
+5862 |
| 3 |
E. coli |
CIP |
-2007 |
-1763 |
-2061 |
-5831 |
+1973 |
+1841 |
+2048 |
+5862 |
| 4 |
E. coli |
GEN |
-1949 |
-1853 |
-2029 |
-5831 |
+2004 |
+1842 |
+2016 |
+5862 |
| 6 |
K. pneumoniae |
AMC |
-584 |
-249 |
-479 |
-1312 |
+605 |
+264 |
+473 |
+1342 |
| 5 |
@@ -1072,8 +1072,8 @@ different bug/drug combinations, you can use the
AMX |
0 |
0 |
-1312 |
-1312 |
+1342 |
+1342 |
@@ -1095,34 +1095,34 @@ different bug/drug combinations, you can use the
| E. coli |
GEN |
-1949 |
-1853 |
-2029 |
-5831 |
+2004 |
+1842 |
+2016 |
+5862 |
| K. pneumoniae |
GEN |
-452 |
-426 |
-434 |
-1312 |
+449 |
+429 |
+464 |
+1342 |
| S. aureus |
GEN |
-1098 |
-1008 |
-1135 |
-3241 |
+1116 |
+1009 |
+1106 |
+3231 |
| S. pneumoniae |
GEN |
0 |
0 |
-1857 |
-1857 |
+1864 |
+1864 |
@@ -1154,7 +1154,7 @@ I (proportion_SI(), equa
own:
+# [1] 0.5870396
Or can be used in conjunction with group_by() and
summarise(), both from the dplyr package:
@@ -1169,19 +1169,19 @@ own:
| Hospital A |
-0.5864297 |
+0.5791485 |
| Hospital B |
-0.5778776 |
+0.5819352 |
| Hospital C |
-0.5783004 |
+0.6098081 |
| Hospital D |
-0.5938144 |
+0.5905316 |
@@ -1206,23 +1206,23 @@ all isolates available for every group (i.e. values S, I or R):
| Hospital A |
-0.5864297 |
-3714 |
+0.5791485 |
+3664 |
| Hospital B |
-0.5778776 |
-4231 |
+0.5819352 |
+4351 |
| Hospital C |
-0.5783004 |
-1871 |
+0.6098081 |
+1876 |
| Hospital D |
-0.5938144 |
-2425 |
+0.5905316 |
+2408 |
@@ -1247,27 +1247,27 @@ therapies very easily:
| Escherichia |
-0.6667810 |
-0.6520322 |
-0.8814955 |
+0.6709314 |
+0.6560901 |
+0.8901399 |
| Klebsiella |
-0.6349085 |
-0.6692073 |
-0.8833841 |
+0.6475410 |
+0.6542474 |
+0.8792846 |
| Staphylococcus |
-0.6599815 |
-0.6497994 |
-0.8707189 |
+0.6601671 |
+0.6576911 |
+0.8895079 |
| Streptococcus |
-0.4787291 |
+0.4812232 |
0.0000000 |
-0.4787291 |
+0.4812232 |
@@ -1295,23 +1295,23 @@ classes, use a antibiotic class selector such as
| Hospital A |
-58.6% |
-36.7% |
+57.9% |
+35.8% |
| Hospital B |
-57.8% |
-36.4% |
+58.2% |
+36.2% |
| Hospital C |
-57.8% |
-37.7% |
+61.0% |
+36.7% |
| Hospital D |
-59.4% |
-36.5% |
+59.1% |
+36.9% |
@@ -1427,18 +1427,18 @@ classes) <mic> and <disk>:
mic_values <- random_mic(size = 100)
mic_values
# Class 'mic'
-# [1] 0.01 >=256 <=0.001 8 0.005 0.005 0.01 1 4
-# [10] >=256 0.0625 4 16 0.01 32 0.01 >=256 32
-# [19] 4 0.0625 0.005 64 128 8 <=0.001 0.25 0.005
-# [28] 0.0625 <=0.001 0.125 0.0625 0.025 0.01 2 32 4
-# [37] 4 128 0.002 <=0.001 0.025 >=256 0.125 0.5 2
-# [46] 0.025 0.005 >=256 16 0.5 2 0.25 0.25 0.25
-# [55] 64 8 <=0.001 8 4 0.0625 <=0.001 0.0625 1
-# [64] 0.0625 0.01 1 0.002 16 <=0.001 0.125 0.005 0.0625
-# [73] 16 0.125 128 0.005 16 64 8 16 <=0.001
-# [82] 16 4 2 0.002 64 8 64 0.5 0.025
-# [91] 1 0.025 1 32 0.002 16 0.125 0.125 16
-# [100] 0.01
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
# Class 'disk'
-# [1] 20 19 27 26 31 31 29 20 28 29 17 25 20 20 26 30 21 26 28 26 29 28 25 17 19
-# [26] 18 25 25 24 21 21 17 25 17 31 18 21 18 21 30 18 29 20 27 29 29 19 25 21 22
-# [51] 30 25 30 21 22 23 25 22 27 19 17 30 28 25 17 19 21 26 18 22 31 27 21 26 20
-# [76] 21 30 24 26 17 31 23 23 23 19 25 31 17 21 23 24 22 29 23 24 21 22 27 27 23
+# [1] 22 30 24 28 31 26 27 25 31 17 20 23 22 30 28 24 20 20 18 31 21 24 19 25 21
+# [26] 19 22 26 22 20 31 26 31 20 17 23 25 31 23 26 24 17 24 21 25 18 26 27 17 17
+# [51] 26 20 20 18 26 24 29 22 28 29 30 21 28 31 30 17 28 17 19 27 24 21 18 21 18
+# [76] 24 30 18 18 24 28 27 17 31 28 29 31 18 20 30 29 31 28 31 19 22 28 28 26 30
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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