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@@ -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 05 April 2026.
methodology remains unchanged. This page was generated on 21 April 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-04-05 | abcd | Escherichia coli | S | S |
| 2026-04-05 | abcd | Escherichia coli | S | R |
| 2026-04-05 | efgh | Escherichia coli | R | S |
| 2026-04-21 | abcd | Escherichia coli | S | S |
| 2026-04-21 | abcd | Escherichia coli | S | R |
| 2026-04-21 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -623,7 +623,8 @@ antibiotic class selectors:
``` r
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
antibiotics = c(aminoglycosides(), carbapenems())
)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
@@ -659,10 +660,11 @@ language to be Spanish using the `language` argument:
``` r
antibiogram(example_isolates,
mo_transform = "gramstain",
antibiotics = aminoglycosides(),
ab_transform = "name",
language = "es")
mo_transform = "gramstain",
antibiotics = aminoglycosides(),
ab_transform = "name",
language = "es"
)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
```
@@ -679,8 +681,9 @@ plus `+` character like this:
``` r
combined_ab <- antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
ab_transform = NULL)
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
ab_transform = NULL
)
combined_ab
```
@@ -705,8 +708,9 @@ on certain columns:
``` r
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward"
)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
@@ -742,8 +746,10 @@ antimicrobial susceptibility patterns.
``` r
example_isolates %>%
wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
minimum = 10) # Recommended threshold: ≥30
wisca(
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
minimum = 10
) # Recommended threshold: ≥30
```
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
@@ -771,8 +777,10 @@ first:
``` r
example_isolates %>%
top_n_microorganisms(n = 10) %>%
group_by(age_group = age_groups(age, c(25, 50, 75)),
gender) %>%
group_by(
age_group = age_groups(age, c(25, 50, 75)),
gender
) %>%
wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
```
@@ -909,17 +917,21 @@ colour-code SIR categories.
``` r
# add a group
my_data$group <- rep(c("A", "B", "C", "D"), each = 25)
my_data$group <- rep(c("A", "B", "C", "D"), each = 25)
ggplot(my_data,
aes(x = group, y = MIC, colour = SIR)) +
ggplot(
my_data,
aes(x = group, y = MIC, colour = SIR)
) +
geom_jitter(width = 0.2, size = 2) +
geom_boxplot(fill = NA, colour = "grey40") +
scale_y_mic() +
scale_colour_sir() +
labs(title = "MIC Distribution and SIR Interpretation",
x = "Sample Groups",
y = "MIC (mg/L)")
labs(
title = "MIC Distribution and SIR Interpretation",
x = "Sample Groups",
y = "MIC (mg/L)"
)
```
![](AMR_files/figure-html/mic_plot-1.png)