Generating antibiograms
@@ -256,117 +171,119 @@
If used inside R Markdown or Quarto, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).
-
+ antimicrobials = c(aminoglycosides(), carbapenems()))
+#> [34mℹ For [48;5;255maminoglycosides()[49m using columns '[1mGEN[22m' (gentamicin), '[1mTOB[22m' (tobramycin), '[1mAMK[22m' (amikacin), and '[1mKAN[22m' (kanamycin)[39m
+#> [34mℹ For [48;5;255mcarbapenems()[49m using columns '[1mIPM[22m' (imipenem) and '[1mMEM[22m' (meropenem)[39m
+#> [31mℹ 502 combinations had less than [48;5;255mminimum = 30[49m results and were ignored[39m
+
-
-
+
+
| CoNS |
-0% (0-8%) |
-86% (82-90%) |
-52% (37-67%) |
-0% (0-8%) |
-52% (37-67%) |
-22% (12-35%) |
+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%) |
-98% (96-99%) |
-100% (99-100%) |
- |
-100% (99-100%) |
-97% (96-99%) |
+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%) |
-0% (0-9%) |
-100% (91-100%) |
-0% (0-9%) |
- |
-0% (0-9%) |
+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%) |
-100% (93-100%) |
- |
-100% (93-100%) |
-90% (79-96%) |
+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%) |
- |
-0% (0-12%) |
- |
-100% (88-100%) |
+P. aeruginosa |
+ |
+100% (88-100%,N=30) |
+ |
+0% (0-12%,N=30) |
+ |
+100% (88-100%,N=30) |
-| P. mirabilis |
- |
-94% (80-99%) |
-94% (79-99%) |
- |
- |
-94% (80-99%) |
+P. mirabilis |
+ |
+94% (80-99%,N=34) |
+94% (79-99%,N=32) |
+ |
+ |
+94% (80-99%,N=34) |
-| S. aureus |
- |
-99% (97-100%) |
- |
- |
- |
-98% (92-100%) |
+S. aureus |
+ |
+99% (97-100%,N=233) |
+ |
+ |
+ |
+98% (92-100%,N=86) |
-| S. epidermidis |
-0% (0-8%) |
-79% (71-85%) |
- |
-0% (0-8%) |
- |
-51% (40-61%) |
+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%) |
- |
- |
- |
-85% (74-93%) |
+S. hominis |
+ |
+92% (84-97%,N=80) |
+ |
+ |
+ |
+85% (74-93%,N=62) |
-| S. pneumoniae |
-0% (0-3%) |
-0% (0-3%) |
- |
-0% (0-3%) |
- |
-0% (0-3%) |
+S. pneumoniae |
+0% (0-3%,N=117) |
+0% (0-3%,N=117) |
+ |
+0% (0-3%,N=117) |
+ |
+0% (0-3%,N=117) |
@@ -374,33 +291,33 @@
antibiogram(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
- mo_transform = "gramstain",
- formatting_type = 14)
+ mo_transform = "gramstain")
+#> [31mℹ 3 combinations had less than [48;5;255mminimum = 30[49m results and were ignored[39m
+
-
-
-
-
+
+
+
+
| Gram-negative |
-88% (85-91%) |
-99% (97-99%) |
-98% (97-99%) |
+88% (85-91%,N=641) |
+99% (97-99%,N=691) |
+98% (97-99%,N=693) |
| Gram-positive |
-86% (82-89%) |
-98% (96-98%) |
-95% (93-97%) |
+86% (82-89%,N=345) |
+98% (96-98%,N=1044) |
+95% (93-97%,N=550) |
@@ -410,27 +327,33 @@
antimicrobials = c("cipro", "tobra", "genta"), # any arbitrary name or code will work
mo_transform = "gramstain",
ab_transform = "name",
- formatting_type = 14,
- language = "uk") # Ukrainian
+ language = "uk") # Ukrainian
+#> [31mℹ 3 combinations had less than [48;5;255mminimum = 30[49m results and were ignored[39m
+
+
+
+
+
+
| Грамнегативні |
-96% (95-98%) |
-96% (94-97%) |
-91% (88-93%) |
+96% (95-98%,N=684) |
+96% (94-97%,N=686) |
+91% (88-93%,N=684) |
| Грампозитивні |
-63% (60-66%) |
-34% (31-38%) |
-77% (74-80%) |
+63% (60-66%,N=1170) |
+34% (31-38%,N=665) |
+77% (74-80%,N=724) |
@@ -480,39 +403,13 @@
# and get their 95% confidence intervals using sir_confidence_interval():
summarise(across(c(GEN, TOB),
list(total_R = resistance,
- conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
-
-
-
-
-| Clinical |
-0.2289362 |
-0.205-0.254 |
-0.3147503 |
-0.284-0.347 |
-
-
-| ICU |
-0.2902655 |
-0.253-0.33 |
-0.4004739 |
-0.353-0.449 |
-
-
-| Outpatient |
-0.2000000 |
-0.131-0.285 |
-0.3676471 |
-0.254-0.493 |
-
-
-
+ conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
+#> # A tibble: 3 × 5
+#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
+#> <chr> <dbl> <chr> <dbl> <chr>
+#> 1 Clinical 0.2289362 0.205-0.254 0.3147503 0.284-0.347
+#> 2 ICU 0.2902655 0.253-0.33 0.4004739 0.353-0.449
+#> 3 Outpatient 0.2 0.131-0.285 0.3676471 0.254-0.493
Or use antimicrobial selectors to select a series of antibiotic columns:
-
-
-
-
-| Clinical |
-0.229 |
-0.315 |
-0.626 |
-1 |
-0.780 |
-
-
-| ICU |
-0.290 |
-0.400 |
-0.662 |
-1 |
-0.857 |
-
-
-| Outpatient |
-0.200 |
-0.368 |
-0.605 |
- |
-0.889 |
-
-
-
+#> [34mℹ For [48;5;255maminoglycosides()[49m using columns '[1mGEN[22m' (gentamicin), '[1mTOB[22m' (tobramycin), '[1mAMK[22m' (amikacin), and '[1mKAN[22m' (kanamycin)[39m
+#> [34mℹ For [48;5;255mpolymyxins()[49m using column '[1mCOL[22m' (colistin)[39m
+#> 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" ([48;5;255mminimum[49m = 30).
+out
+#> # A tibble: 3 × 6
+#> ward GEN TOB AMK KAN COL
+#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
+#> 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956
+#> 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144
+#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889
-
-
-
-
-
-
-
-
-
-
-
-
-| Clinical |
-0.229 |
-0.315 |
-0.626 |
-1 |
-0.780 |
-
-
-| ICU |
-0.290 |
-0.400 |
-0.662 |
-1 |
-0.857 |
-
-
-| Outpatient |
-0.200 |
-0.368 |
-0.605 |
- |
-0.889 |
-
-
-
+out %>% set_ab_names()
+#> # A tibble: 3 × 6
+#> ward gentamicin tobramycin amikacin kanamycin colistin
+#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
+#> 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956
+#> 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144
+#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889
# transform the antibiotic column to ATC codes:
-out %>% set_ab_names(property = "atc")
-
-
-
-
-
-
-
-
-
-
-
-| Clinical |
-0.229 |
-0.315 |
-0.626 |
-1 |
-0.780 |
-
-
-| ICU |
-0.290 |
-0.400 |
-0.662 |
-1 |
-0.857 |
-
-
-| Outpatient |
-0.200 |
-0.368 |
-0.605 |
- |
-0.889 |
-
-
-
+out %>% set_ab_names(property = "atc")
+#> # A tibble: 3 × 6
+#> ward J01GB03 J01GB01 J01GB06 J01GB04 J01XB01
+#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
+#> 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956
+#> 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144
+#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889
@@ -714,7 +512,7 @@
Partners
-
The development of this package is part of, related to, or made possible by the following non-profit organisations and initiatives:
+
The initial development of this package was part of, related to, or made possible by the following non-profit organisations and initiatives:
diff --git a/news/index.html b/news/index.html
index bfb3d89c8..659bf4c7a 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9249
+
2.1.1.9250
-
AMR 2.1.1.9249
+
AMR 2.1.1.9250
(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.)
-
A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
+
A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the University of Prince Edward Island’s Atlantic Veterinary College, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
-
Breaking
+
Breaking
- Dataset
antibiotics has been renamed to antimicrobials as the data set contains more than just antibiotics. Using antibiotics will still work, but now returns a warning.
- Removed all functions and references that used the deprecated
rsi class, which were all replaced with their sir equivalents over two years ago.
- Functions
resistance_predict() and sir_predict() is now deprecated and will be removed in a future version. Use the tidymodels framework instead, for which we wrote a basic introduction.
-
New
+
New
-
One Health implementation
- Function
as.sir() now has extensive support for veterinary breakpoints from CLSI. Use breakpoint_type = "animal" and set the host argument to a variable that contains animal species names.
@@ -117,7 +117,7 @@
-
Changed
+
Changed
- SIR interpretation
- It is now possible to use column names for arguments
guideline, ab, mo, and uti: as.sir(..., ab = "column1", mo = "column2", uti = "column3"). This greatly improves the flexibility for users.
- Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.
@@ -198,7 +198,7 @@
- Added console colours support of
sir class for Positron
-
Other
+
Other
- New website domain: https://amr-for-r.org! The old domain (http://amr-for-r.org) will remain to work.
- Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
- Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
@@ -208,7 +208,7 @@
- Stopped support for SAS (
.xpt) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.
-
Older Versions
+
Older Versions
This changelog only contains changes from AMR v3.0 (March 2025) and later.
- For prior v2 versions, please see our v2 archive.
- For prior v1 versions, please see our v1 archive.
diff --git a/pkgdown.yml b/pkgdown.yml
index 354a2451d..37da980c3 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
PCA: PCA.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
-last_built: 2025-04-20T15:53Z
+last_built: 2025-04-21T13:41Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles
diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html
index 145a2f02b..77c4138b6 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9249
+ 2.1.1.9250