diff --git a/DESCRIPTION b/DESCRIPTION
index 3522c7b49..7bced315a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 2.1.1.9261
+Version: 2.1.1.9262
Date: 2025-04-29
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 1bdc13fb4..558f5b009 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9261
+# AMR 2.1.1.9262
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*
diff --git a/data-raw/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R
index df4516d95..e124be975 100644
--- a/data-raw/_pre_commit_checks.R
+++ b/data-raw/_pre_commit_checks.R
@@ -657,7 +657,7 @@ if (files_changed()) {
}
# Update index.md and README.md -------------------------------------------
-if (files_changed("man/microorganisms.Rd") | files_changed("man/antimicrobials.Rd") | files_changed("man/clinical_breakpoints.Rd") | files_changed("man/antibiogram.Rd")) {
+if (files_changed("man/microorganisms.Rd") | files_changed("man/antimicrobials.Rd") | files_changed("man/clinical_breakpoints.Rd") | files_changed("man/antibiogram.Rd") | files_changed("R/antibiogram.R")) {
usethis::ui_info("Rendering {usethis::ui_field('index.md')} and {usethis::ui_field('README.md')}")
suppressWarnings(rmarkdown::render("index.Rmd", quiet = TRUE))
suppressWarnings(rmarkdown::render("README.Rmd", quiet = TRUE))
diff --git a/index.md b/index.md
index 2e9f40a5e..aec3d208f 100644
--- a/index.md
+++ b/index.md
@@ -155,10 +155,9 @@ example_isolates %>%
#> ℹ Using column 'mo' as input for mo_fullname()
#> ℹ Using column 'mo' as input for mo_is_gram_negative()
#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()
-#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
-#> Phenotypes' v1.2 (2023). This note will be shown once per session.
-#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
-#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
+#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023). This note will be shown once per
+#> session.
+#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
@@ -196,23 +195,23 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
``` r
antibiogram(example_isolates,
antimicrobials = 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)
+#> ℹ 502 combinations had less than minimum = 30 results and were ignored
```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
|:---|:---|:---|:---|:---|:---|:---|
| CoNS | 0% (0-8%,N=43) | 86% (82-90%,N=309) | 52% (37-67%,N=48) | 0% (0-8%,N=43) | 52% (37-67%,N=48) | 22% (12-35%,N=55) |
-| E. coli | 100% (98-100%,N=171) | 98% (96-99%,N=460) | 100% (99-100%,N=422) | | 100% (99-100%,N=418) | 97% (96-99%,N=462) |
-| E. faecalis | 0% (0-9%,N=39) | 0% (0-9%,N=39) | 100% (91-100%,N=38) | 0% (0-9%,N=39) | | 0% (0-9%,N=39) |
-| K. pneumoniae | | 90% (79-96%,N=58) | 100% (93-100%,N=51) | | 100% (93-100%,N=53) | 90% (79-96%,N=58) |
-| P. aeruginosa | | 100% (88-100%,N=30) | | 0% (0-12%,N=30) | | 100% (88-100%,N=30) |
-| P. mirabilis | | 94% (80-99%,N=34) | 94% (79-99%,N=32) | | | 94% (80-99%,N=34) |
-| S. aureus | | 99% (97-100%,N=233) | | | | 98% (92-100%,N=86) |
-| S. epidermidis | 0% (0-8%,N=44) | 79% (71-85%,N=163) | | 0% (0-8%,N=44) | | 51% (40-61%,N=89) |
-| S. hominis | | 92% (84-97%,N=80) | | | | 85% (74-93%,N=62) |
-| S. pneumoniae | 0% (0-3%,N=117) | 0% (0-3%,N=117) | | 0% (0-3%,N=117) | | 0% (0-3%,N=117) |
+| *E. coli* | 100% (98-100%,N=171) | 98% (96-99%,N=460) | 100% (99-100%,N=422) | NA | 100% (99-100%,N=418) | 97% (96-99%,N=462) |
+| *E. faecalis* | 0% (0-9%,N=39) | 0% (0-9%,N=39) | 100% (91-100%,N=38) | 0% (0-9%,N=39) | NA | 0% (0-9%,N=39) |
+| *K. pneumoniae* | NA | 90% (79-96%,N=58) | 100% (93-100%,N=51) | NA | 100% (93-100%,N=53) | 90% (79-96%,N=58) |
+| *P. aeruginosa* | NA | 100% (88-100%,N=30) | NA | 0% (0-12%,N=30) | NA | 100% (88-100%,N=30) |
+| *P. mirabilis* | NA | 94% (80-99%,N=34) | 94% (79-99%,N=32) | NA | NA | 94% (80-99%,N=34) |
+| *S. aureus* | NA | 99% (97-100%,N=233) | NA | NA | NA | 98% (92-100%,N=86) |
+| *S. epidermidis* | 0% (0-8%,N=44) | 79% (71-85%,N=163) | NA | 0% (0-8%,N=44) | NA | 51% (40-61%,N=89) |
+| *S. hominis* | NA | 92% (84-97%,N=80) | NA | NA | NA | 85% (74-93%,N=62) |
+| *S. pneumoniae* | 0% (0-3%,N=117) | 0% (0-3%,N=117) | NA | 0% (0-3%,N=117) | NA | 0% (0-3%,N=117) |
In combination antibiograms, it is clear that combined antimicrobials
yield higher empiric coverage:
@@ -221,6 +220,7 @@ yield higher empiric coverage:
antibiogram(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain")
+#> ℹ 3 combinations had less than minimum = 30 results and were ignored
```
| Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
@@ -238,6 +238,7 @@ antibiogram(example_isolates,
mo_transform = "gramstain",
ab_transform = "name",
language = "uk") # Ukrainian
+#> ℹ 3 combinations had less than minimum = 30 results and were ignored
```
| Збудник | Гентаміцин | Тобраміцин | Ципрофлоксацин |
@@ -321,15 +322,13 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
-#> 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 polymyxins() using column 'COL' (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
-#> ! Introducing NA: only 23 results available for KAN in group: ward =
-#> "Outpatient" (minimum = 30).
+#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (minimum = 30).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL