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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 18 March 2026.
methodology remains unchanged. This page was generated on 20 March 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-03-18 | abcd | Escherichia coli | S | S |
| 2026-03-18 | abcd | Escherichia coli | S | R |
| 2026-03-18 | efgh | Escherichia coli | R | S |
| 2026-03-20 | abcd | Escherichia coli | S | S |
| 2026-03-20 | abcd | Escherichia coli | S | R |
| 2026-03-20 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -169,8 +169,9 @@ our_data$bacteria <- as.mo(our_data$bacteria, info = TRUE)
#> ℹ Retrieved values from the `microorganisms.codes` data set for "ESCCOL",
#> "KLEPNE", "STAAUR", and "STRPNE".
#> ℹ Microorganism translation was uncertain for four microorganisms. Run
#> `mo_uncertainties()` to review these uncertainties, or use
#> `add_custom_microorganisms()` to add custom entries.
#> `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to review these
#> uncertainties, or use `add_custom_microorganisms()`
#> (`?AMR::add_custom_microorganisms()`) to add custom entries.
```
Apparently, there was some uncertainty about the translation to
@@ -179,46 +180,43 @@ taxonomic codes. Let’s check this:
``` r
mo_uncertainties()
#> Matching scores are based on the resemblance between the input and the full
#> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.
#> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`
#> (`?AMR::mo_matching_score()`).
#> Colour keys: 0.000-0.549 0.550-0.649 0.650-0.749 0.750-1.000
#>
#> --------------------------------------------------------------------------------
#> -------------------------------------------------------------------------------
#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli
#> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii
#> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591),
#> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae
#> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae
#> dissolvens (0.565)
#> --------------------------------------------------------------------------------
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli (0.643),
#> Escherichia coli expressing (0.611), Enterobacter cowanii (0.600), Enterococcus
#> columbae (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus
#> (0.577), Enterobacter cloacae cloacae (0.571), Enterobacter cloacae complex
#> (0.571), and Enterobacter cloacae dissolvens (0.565)
#> -------------------------------------------------------------------------------
#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)
#> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella
#> pneumoniae ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688),
#> Klebsiella pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii
#> (0.500), Klebsiella planticola (0.500), Kingella potus (0.400),
#> Kluyveromyces pseudotropicale (0.386), Kluyveromyces pseudotropicalis
#> (0.363), and Kosakonia pseudosacchari (0.361)
#> --------------------------------------------------------------------------------
#> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella pneumoniae
#> ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688), Klebsiella
#> pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii (0.500), Klebsiella
#> planticola (0.500), Kingella potus (0.400), Kluyveromyces pseudotropicale
#> (0.386), Kluyveromyces pseudotropicalis (0.363), and Kosakonia pseudosacchari
#> (0.361)
#> -------------------------------------------------------------------------------
#> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690)
#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus
#> argenteus (0.625), Staphylococcus aureus anaerobius (0.625),
#> Staphylococcus auricularis (0.615), Salmonella Aurelianis (0.595),
#> Salmonella Aarhus (0.588), Salmonella Amounderness (0.587),
#> Staphylococcus argensis (0.587), Streptococcus australis (0.587), and
#> Salmonella choleraesuis arizonae (0.562)
#> --------------------------------------------------------------------------------
#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus argenteus
#> (0.625), Staphylococcus aureus anaerobius (0.625), Staphylococcus auricularis
#> (0.615), Salmonella Aurelianis (0.595), Salmonella Aarhus (0.588), Salmonella
#> Amounderness (0.587), Staphylococcus argensis (0.587), Streptococcus australis
#> (0.587), and Salmonella choleraesuis arizonae (0.562)
#> -------------------------------------------------------------------------------
#> "S. pneumoniae" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)
#> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus
#> phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545),
#> Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans
#> (0.533), Staphylococcus pseudintermedius (0.532), Serratia
#> proteamaculans proteamaculans (0.526), Streptococcus gallolyticus
#> pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus
#> periodonticum (0.519)
#>
#> Only the first 10 other matches of each record are shown. Run
#> `print(mo_uncertainties(), n = ...)` to view more entries, or save
#> `mo_uncertainties()` to an object.
#> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus phocae
#> salmonis (0.552), Serratia proteamaculans quinovora (0.545), Streptococcus
#> pseudoporcinus (0.536), Staphylococcus piscifermentans (0.533), Staphylococcus
#> pseudintermedius (0.532), Serratia proteamaculans proteamaculans (0.526),
#> Streptococcus gallolyticus pasteurianus (0.526), Salmonella Portanigra (0.524),
#> and Streptococcus periodonticum (0.519)
#> ℹ Only the first 10 other matches of each record are shown. Run
#> `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view
#> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an
#> object.
```
That’s all good.
@@ -317,14 +315,13 @@ our_data <- our_data %>%
mutate(first = first_isolate(info = TRUE))
#> ℹ Determining first isolates using an episode length of 365 days
#> ℹ Using column 'bacteria' as input for `col_mo`.
#> ℹ Column 'first' is SIR eligible (despite only having empty values), since
#> it seems to be cefozopran (ZOP)
#> ℹ Column 'first' is SIR eligible (despite only having empty values), since it
#> seems to be cefozopran (ZOP)
#> ℹ Using column 'date' as input for `col_date`.
#> ℹ Using column 'patient_id' as input for `col_patient_id`.
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold
#> of 2
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a
#> microbial ID was available)
#> microbial ID was available)
```
So only 91% is suitable for resistance analysis! We can now filter on it
@@ -628,8 +625,8 @@ antibiotic class selectors:
``` r
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
```
@@ -667,8 +664,8 @@ antibiogram(example_isolates,
antibiotics = aminoglycosides(),
ab_transform = "name",
language = "es")
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
```
| Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina |
@@ -711,8 +708,8 @@ on certain columns:
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
```
@@ -844,9 +841,10 @@ These functions can be used on their own:
``` r
our_data_1st %>% resistance(AMX)
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
#> considers the 'I' category susceptible. Set the `guideline` argument or the
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::AMR-options`).
#> ℹ This message will be shown once per session.
#> [1] 0.4203377
```