P281424/AMR
1
0 Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-11-16 00:10:57 +01:00
Code Releases Activity

(v3.0.1.9108) Fix the seed in index.Rmd, so that the WISCA output in index.md no longer changes on every build

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends committed 2026-10-10 09:14:29 +02:00
1 parent 3eeabf542a
commit 6a778daeb8
4 files changed
+8 -6
Download Patch File Download Diff File Expand all files Collapse all files

No files matched your search

DESCRIPTION
+1 -1
View File
@@ -1,5 +1,5 @@
Package: AMR
Version: 3.0.1.9107
Version: 3.0.1.9108
Date: 2026-10-10
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
NEWS.md
+1 -1
View File
@@ -1,4 +1,4 @@
# AMR 3.0.1.9107
# AMR 3.0.1.9108
Planned as v3.1.0, mid October 2026.
index.Rmd
+2
View File
@@ -15,6 +15,8 @@ knitr::opts_chunk$set(
)
options(width = 100)
AMR:::reset_all_thrown_messages()
# wisca() uses Monte Carlo simulations, so fix the seed to keep the output (and index.md) stable between builds
set.seed(1)
```
# The `AMR` Package for R <a href="https://amr-for-r.org/"><img src="./logo.svg" align="right" height="139" /></a>
index.md
+4 -4
View File
@@ -225,7 +225,7 @@ wisca(example_isolates,
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:------------------------|:-------------------------------------|:-------------------------------------|
| 70% (64.7-75.3%) | 93.6% (92.1-95%) | 89.8% (86.7-92.4%) |
| 69.8% (64.5-74.7%) | 93.6% (92.1-95%) | 89.9% (87-92.5%) |
WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates:
@@ -240,9 +240,9 @@ wisca(example_isolates,
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:----------------|:------------------------|:-------------------------------------|:-------------------------------------|
| Clinical | 74.7% (68.7-80.4%) | 93.6% (91.9-95.2%) | 90.4% (86.9-93.1%) |
| ICU | 56.9% (48.5-65.6%) | 86.7% (83.2-89.7%) | 83% (78.2-87.2%) |
| Outpatient | 57.4% (46-68.9%) | 76.6% (70.7-82.3%) | 67.5% (57.2-77.3%) |
| Clinical | 74.6% (69.1-80.1%) | 93.7% (92.1-95.1%) | 90.3% (87-93.1%) |
| ICU | 56.9% (48.3-66%) | 86.7% (83.5-89.8%) | 83% (77.9-87.4%) |
| Outpatient | 57.7% (46.5-69.3%) | 76.6% (70.5-82.2%) | 67.8% (56.9-77.5%) |
**For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time: