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index.md
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index.md
@@ -3,9 +3,9 @@
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- Provides an **all-in-one solution** for antimicrobial resistance (AMR)
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data analysis in a One Health approach
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- Peer-reviewed, used in over 175 countries, available in 28 languages
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- Generates **antibiograms** - traditional, combined, syndromic, and
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even WISCA
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- Provides the **full microbiological taxonomy** of ~79 000 distinct
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- Generates **antibiograms** - WISCA for empiric coverage estimates, or
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traditional/syndromic for AMR surveillance
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- Provides the **full microbiological taxonomy** of ~97 000 distinct
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species and extensive info of ~620 antimicrobial drugs
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- Applies **CLSI 2011-2026** and **EUCAST 2011-2026** clinical and
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veterinary breakpoints, and ECOFFs, for MIC and disk zone
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@@ -49,7 +49,7 @@ formed the basis of two PhD theses ([DOI
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10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and
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[DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
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After installing this package, R knows [**~79 000 distinct microbial
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After installing this package, R knows [**~97 000 distinct microbial
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species**](https://amr-for-r.org/reference/microorganisms.md) (updated
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June 2024) and all [**~620 antimicrobial and antiviral
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drugs**](https://amr-for-r.org/reference/antimicrobials.md) by name and
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@@ -117,26 +117,24 @@ example_isolates %>%
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#> ℹ Using column mo as input for `mo_fullname()`
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#> ℹ Using column mo as input for `mo_is_gram_negative()`
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#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
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#> ℹ Determining intrinsic resistance based on 'EUCAST Expected
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#> Resistant Phenotypes' v1.2 (2023). This note will be shown
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#> once per session.
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#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
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#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
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#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
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#> (meropenem)
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#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
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#> Phenotypes' v1.2 (2023). This note will be shown once per session.
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#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
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#> (amikacin), and KAN (kanamycin)
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#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
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#> # A tibble: 35 × 7
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#> bacteria GEN TOB AMK KAN IPM MEM
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#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
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#> 1 Pseudomonas aer… I S NA R S NA
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#> 2 Pseudomonas aer… I S NA R S NA
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#> 3 Pseudomonas aer… I S NA R S NA
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#> 4 Pseudomonas aer… S S S R NA S
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#> 5 Pseudomonas aer… S S S R S S
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#> 6 Pseudomonas aer… S S S R S S
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#> 7 Stenotrophomona… R R R R R R
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#> 8 Pseudomonas aer… S S S R NA S
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#> 9 Pseudomonas aer… S S S R NA S
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#> 10 Pseudomonas aer… S S S R S S
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#> bacteria GEN TOB AMK KAN IPM MEM
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#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
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#> 1 Pseudomonas aeruginosa I S NA R S NA
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#> 2 Pseudomonas aeruginosa I S NA R S NA
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#> 3 Pseudomonas aeruginosa I S NA R S NA
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#> 4 Pseudomonas aeruginosa S S S R NA S
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#> 5 Pseudomonas aeruginosa S S S R S S
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#> 6 Pseudomonas aeruginosa S S S R S S
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#> 7 Stenotrophomonas maltophilia R R R R R R
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#> 8 Pseudomonas aeruginosa S S S R NA S
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#> 9 Pseudomonas aeruginosa S S S R NA S
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#> 10 Pseudomonas aeruginosa S S S R S S
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#> # ℹ 25 more rows
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```
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@@ -167,10 +165,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
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antibiogram(example_isolates,
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antimicrobials = c(aminoglycosides(), carbapenems()))
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#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
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#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
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#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
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#> (meropenem)
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#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
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#> (amikacin), and KAN (kanamycin)
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#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
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```
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| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
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@@ -275,18 +272,16 @@ example_isolates %>%
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summarise(across(c(GEN, TOB),
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list(total_R = resistance,
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conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
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#> ℹ `resistance()` assumes the EUCAST guideline and thus
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#> considers the 'I' category susceptible. Set the `guideline`
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#> argument or the `AMR_guideline` option to either "CLSI" or
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#> "EUCAST", see `?AMR-options`.
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#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
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#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
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#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
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#> ℹ This message will be shown once per session.
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#> # A tibble: 3 × 5
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#> ward GEN_total_R GEN_conf_int TOB_total_R
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#> <chr> <dbl> <chr> <dbl>
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#> 1 Clinical 0.229 0.205-0.254 0.315
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#> 2 ICU 0.290 0.253-0.33 0.400
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#> 3 Outpatient 0.2 0.131-0.285 0.368
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#> # ℹ 1 more variable: TOB_conf_int <chr>
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#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
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#> <chr> <dbl> <chr> <dbl> <chr>
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#> 1 Clinical 0.229 0.205-0.254 0.315 0.284-0.347
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#> 2 ICU 0.290 0.253-0.33 0.400 0.353-0.449
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#> 3 Outpatient 0.2 0.131-0.285 0.368 0.254-0.493
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```
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Or use [antimicrobial
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@@ -304,16 +299,15 @@ out <- example_isolates %>%
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# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
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summarise(across(c(aminoglycosides(), polymyxins()),
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resistance))
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#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
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#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
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#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
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#> (amikacin), and KAN (kanamycin)
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#> ℹ For `polymyxins()` using column COL (colistin)
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#> Warning: There was 1 warning in `summarise()`.
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#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()),
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#> resistance)`.
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#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
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#> ℹ In group 3: `ward = "Outpatient"`.
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#> Caused by warning:
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#> ! Introducing NA: only 23 results available for KAN in group:
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#> ward = "Outpatient" (whilst `minimum = 30`).
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#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"
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#> (whilst `minimum = 30`).
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out
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#> # A tibble: 3 × 6
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#> ward GEN TOB AMK KAN COL
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@@ -328,12 +322,11 @@ out
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# transform the antibiotic columns to names:
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out %>% set_ab_names()
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#> # A tibble: 3 × 6
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#> ward gentamicin tobramycin amikacin kanamycin
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#> <chr> <dbl> <dbl> <dbl> <dbl>
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#> 1 Clinical 0.229 0.315 0.626 1
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#> 2 ICU 0.290 0.400 0.662 1
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#> 3 Outpatient 0.2 0.368 0.605 NA
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#> # ℹ 1 more variable: colistin <dbl>
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#> ward gentamicin tobramycin amikacin kanamycin colistin
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#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
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#> 1 Clinical 0.229 0.315 0.626 1 0.780
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#> 2 ICU 0.290 0.400 0.662 1 0.857
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#> 3 Outpatient 0.2 0.368 0.605 NA 0.889
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```
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``` r
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