P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-05-31 12:21:40 +02:00
Code Releases Activity

Built site for AMR@3.0.1.9050: 8261b91

Browse Source
This commit is contained in:
github-actions
2026-04-25 12:49:42 +00:00
parent cc4e9bab4b
commit e12355b4a8
16 changed files with 127 additions and 113 deletions
Download Patch File Download Diff File Expand all files Collapse all files

50
articles/AMR.md
View File

@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 24 April 2026.
methodology remains unchanged. This page was generated on 25 April 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-04-24 | abcd | Escherichia coli | S | S |
| 2026-04-24 | abcd | Escherichia coli | S | R |
| 2026-04-24 | efgh | Escherichia coli | R | S |
| 2026-04-25 | abcd | Escherichia coli | S | S |
| 2026-04-25 | abcd | Escherichia coli | S | R |
| 2026-04-25 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -367,27 +367,27 @@ and `sir` classes that we now have in our data set:
``` r
summary(our_data_1st)
#> patient_id hospital date
#> Length:2724 Length:2724 Min. :2011-01-01
#> Class :character Class :character 1st Qu.:2013-04-07
#> Mode :character Mode :character Median :2015-06-03
#> Mean :2015-06-09
#> 3rd Qu.:2017-08-11
#> Max. :2019-12-27
#> bacteria AMX AMC
#> Class :mo Class:sir Class:sir
#> <NA> :0 %S :41.6% (n=1133) %S :52.6% (n=1432)
#> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
#> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333)
#> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959)
#> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0)
#> CIP GEN first
#> Class:sir Class:sir Mode:logical
#> %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724
#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
#> %I : 6.5% (n=176) %I : 3.0% (n=82)
#> %R :41.0% (n=1117) %R :36.0% (n=981)
#> %NI : 0.0% (n=0) %NI : 0.0% (n=0)
#> patient_id hospital date bacteria
#> Length :2724 Length :2724 Min. :2011-01-01 Class :mo
#> N.unique : 260 N.unique : 3 1st Qu.:2013-04-07 <NA> :0
#> N.blank : 0 N.blank : 0 Median :2015-06-03 Unique:4
#> Min.nchar: 2 Min.nchar: 1 Mean :2015-06-09 #1 :B_ESCHR_COLI
#> Max.nchar: 3 Max.nchar: 1 3rd Qu.:2017-08-11 #2 :B_STPHY_AURS
#> Max. :2019-12-27 #3 :B_STRPT_PNMN
#> AMX AMC CIP
#> Class:sir Class:sir Class:sir
#> %S :41.6% (n=1133) %S :52.6% (n=1432) %S :52.5% (n=1431)
#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0)
#> %I :16.4% (n=446) %I :12.2% (n=333) %I : 6.5% (n=176)
#> %R :42.0% (n=1145) %R :35.2% (n=959) %R :41.0% (n=1117)
#> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0)
#> GEN first
#> Class:sir Mode:logical
#> %S :61.0% (n=1661) TRUE:2724
#> %SDD : 0.0% (n=0)
#> %I : 3.0% (n=82)
#> %R :36.0% (n=981)
#> %NI : 0.0% (n=0)
glimpse(our_data_1st)
#> Rows: 2,724