#> Groups (n=4, named as 'order'): diff --git a/articles/PCA.md b/articles/PCA.md index 9e63716e5..bf7e4a5f2 100644 --- a/articles/PCA.md +++ b/articles/PCA.md @@ -117,7 +117,7 @@ summary(pca_result) #> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" #> Importance of components: #> PC1 PC2 PC3 PC4 PC5 PC6 PC7 -#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16 +#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00 #> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00 ``` diff --git a/articles/WHONET.html b/articles/WHONET.html index 01042ba59..cc46fb5a6 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/articles/WISCA.html b/articles/WISCA.html index 71ae44814..359af3146 100644 --- a/articles/WISCA.html +++ b/articles/WISCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/articles/datasets.html b/articles/datasets.html index b9116b4db..b04fc123b 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 @@ -80,7 +80,7 @@ Download data sets for download / own use - 04 March 2026 + 06 March 2026 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index d097f7a1c..991d2240e 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/authors.html b/authors.html index 788cbb2de..c9eb1eff5 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/index.html b/index.html index 0ce294e7d..07f08e80b 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/llms.txt b/llms.txt index a48abdabb..d4f280fb0 100644 --- a/llms.txt +++ b/llms.txt @@ -501,8 +501,9 @@ to add your own custom microorganisms to this package. [`mo_renamed()`](https://amr-for-r.org/reference/as.mo.md) [`mo_failures()`](https://amr-for-r.org/reference/as.mo.md) [`mo_reset_session()`](https://amr-for-r.org/reference/as.mo.md) - [`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md) : - Transform Arbitrary Input to Valid Microbial Taxonomy + [`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md) + [`NA_mo_`](https://amr-for-r.org/reference/as.mo.md) : Transform + Arbitrary Input to Valid Microbial Taxonomy - [`mo_name()`](https://amr-for-r.org/reference/mo_property.md) [`mo_fullname()`](https://amr-for-r.org/reference/mo_property.md) [`mo_shortname()`](https://amr-for-r.org/reference/mo_property.md) @@ -557,8 +558,9 @@ from clinical text records, using - [`as.ab()`](https://amr-for-r.org/reference/as.ab.md) [`is.ab()`](https://amr-for-r.org/reference/as.ab.md) - [`ab_reset_session()`](https://amr-for-r.org/reference/as.ab.md) : - Transform Input to an Antibiotic ID + [`ab_reset_session()`](https://amr-for-r.org/reference/as.ab.md) + [`NA_ab_`](https://amr-for-r.org/reference/as.ab.md) : Transform Input + to an Antibiotic ID - [`ab_name()`](https://amr-for-r.org/reference/ab_property.md) [`ab_cid()`](https://amr-for-r.org/reference/ab_property.md) [`ab_synonyms()`](https://amr-for-r.org/reference/ab_property.md) diff --git a/news/index.html b/news/index.html index c34c8aa37..acb1bbbf4 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 @@ -49,9 +49,9 @@ -AMR 3.0.1.9023 +AMR 3.0.1.9026 -New +New Integration with the tidymodels framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via recipes step_mic_log2() to transform <mic> columns with log2, and step_sir_numeric() to convert <sir> columns to numeric @@ -70,7 +70,6 @@ Data set esbl_isolates to practise with AMR modelling AMR selectors peptides(), phosphonics() and spiropyrimidinetriones() -Antimicrobials in the antimicrobials data set: ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR) Support for Wildtype (WT) / Non-wildtype (NWT) in as.sir(), all plotting functions, and all susceptibility/resistance functions. as.sir() gained an argument as_wt_nwt, which defaults to TRUE only when breakpoint_type = "ECOFF" (#254) @@ -80,11 +79,12 @@ interpretive_rules(), which allows future implementation of CLSI interpretive rules (#235) -eucast_rules() has become a wrapper around that function. +eucast_rules() has become a wrapper around that function +Two new NA objects, NA_ab_ and NA_mo_, analogous to base R’s NA_character_ and NA_integer_, for use in pipelines that require typed missing values -Fixes +Fixes Fixed a bug in as.ab() where certain AB codes containing “PH” or “TH” (such as ETH, MTH, PHE, PHN, STH, THA, THI1) would incorrectly return NA when combined in a vector with any untranslatable value (#245) Fixed a bug in antibiogram() for when no antimicrobials are set Fixed a bug in as.sir() where for numeric input the arguments S, I, and R would not be considered (#244) @@ -94,7 +94,7 @@ Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256) -Updates +Updates susceptibility() and resistance() gained the argument guideline, which defaults to EUCAST, for interpreting the ‘I’ category correctly. @@ -103,7 +103,7 @@ antimicrobials$group is now a list instead of a character, to contain any group the drug is in (#246) ab_group() gained an argument all_groups to return all groups the antimicrobial drug is in (#246) -Added taniborbactam (TAN) and cefepime/taniborbactam (FTA) to the antimicrobials data set +Added to the antimicrobials data set: cefepime/taniborbactam (FTA), ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), taniborbactam (TAN), thiostrepton (THS), xeruborbactam (XER), and zorbamycin (ZOR) Added explaining message to as.sir() when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244) Updated handling of capped MIC values (<, <=, >, >=) in as.sir() in the argument capped_mic_handling: (#243) Introduced four clearly defined options: "none", "conservative" (default), "standard", and "lenient" diff --git a/news/index.md b/news/index.md index f9764b8d0..7aa46f76a 100644 --- a/news/index.md +++ b/news/index.md @@ -1,6 +1,6 @@ # Changelog -## AMR 3.0.1.9023 +## AMR 3.0.1.9026 #### New @@ -23,9 +23,6 @@ [`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md) and [`spiropyrimidinetriones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md) -- Antimicrobials in the `antimicrobials` data set: ceftibuten/avibactam - (`CTA`), kasugamycin (`KAS`), ostreogrycin (`OST`), thiostrepton - (`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`) - Support for Wildtype (WT) / Non-wildtype (NWT) in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), all plotting functions, and all susceptibility/resistance functions. @@ -41,7 +38,10 @@ which allows future implementation of CLSI interpretive rules ([\#235](https://github.com/msberends/AMR/issues/235)) - [`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md) - has become a wrapper around that function. + has become a wrapper around that function +- Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R’s + `NA_character_` and `NA_integer_`, for use in pipelines that require + typed missing values #### Fixes @@ -82,8 +82,10 @@ - [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) gained an argument `all_groups` to return all groups the antimicrobial drug is in ([\#246](https://github.com/msberends/AMR/issues/246)) -- Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the - `antimicrobials` data set +- Added to the `antimicrobials` data set: cefepime/taniborbactam + (`FTA`), ceftibuten/avibactam (`CTA`), kasugamycin (`KAS`), + ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), + xeruborbactam (`XER`), and zorbamycin (`ZOR`) - Added explaining message to [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) diff --git a/pkgdown.yml b/pkgdown.yml index 52282ba06..a67250689 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-03-04T08:06Z +last_built: 2026-03-06T11:51Z 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 d39775da3..7fa7a3146 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 144ec05f7..1832a4c7c 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'>AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/reference/AMR.html b/reference/AMR.html index bb8a5f376..e0da547fe 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/reference/NA_ab_.html b/reference/NA_ab_.html new file mode 100644 index 000000000..cef95015e --- /dev/null +++ b/reference/NA_ab_.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/NA_mo_.html b/reference/NA_mo_.html new file mode 100644 index 000000000..626779946 --- /dev/null +++ b/reference/NA_mo_.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 318d1cd02..5b7ab225b 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/reference/WHONET.html b/reference/WHONET.html index b4d38c9f9..c43c89a64 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 2defa0902..8ce1e6666 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/reference/ab_property.html b/reference/ab_property.html index 5e62071de..cdf26a9f8 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 6af469fb7..a134ac5f0 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 268d17ef5..83657a8fa 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 diff --git a/reference/age.html b/reference/age.html index 85feaf7e9..e2a132711 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9023 + 3.0.1.9026 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1980-02-27 46 46.01370 19 -#> 2 1953-07-26 72 72.60548 46 -#> 3 1949-09-02 76 76.50137 50 -#> 4 1986-08-03 39 39.58356 13 -#> 5 1932-11-19 93 93.28767 67 -#> 6 1949-03-30 76 76.92877 50 -#> 7 1996-06-23 29 29.69589 3 -#> 8 1963-09-16 62 62.46301 36 -#> 9 1952-05-16 73 73.80000 47 -#> 10 1952-11-14 73 73.30137 47 +#> 1 1980-02-27 46 46.01918 19 +#> 2 1953-07-26 72 72.61096 46 +#> 3 1949-09-02 76 76.50685 50 +#> 4 1986-08-03 39 39.58904 13 +#> 5 1932-11-19 93 93.29315 67 +#> 6 1949-03-30 76 76.93425 50 +#> 7 1996-06-23 29 29.70137 3 +#> 8 1963-09-16 62 62.46849 36 +#> 9 1952-05-16 73 73.80548 47 +#> 10 1952-11-14 73 73.30685 47
vignettes/datasets.Rmd
datasets.Rmd
recipes
step_mic_log2()
<mic>
step_sir_numeric()
<sir>
esbl_isolates
peptides()
phosphonics()
spiropyrimidinetriones()
antimicrobials
CTA
KAS
OST
THS
XER
ZOR
as.sir()
as_wt_nwt
TRUE
breakpoint_type = "ECOFF"
interpretive_rules()
eucast_rules()
NA
NA_ab_
NA_mo_
NA_character_
NA_integer_
as.ab()
ETH
MTH
PHE
PHN
STH
THA
THI1
antibiogram()
S
I
R
susceptibility()
resistance()
guideline
antimicrobials$group
list
character
ab_group()
all_groups
TAN
FTA
<
<=
>
>=
capped_mic_handling
"none"
"conservative"
"standard"
"lenient"
Use the ab_* functions to get properties based on the returned antibiotic ID, see Examples.
ab_*
Note: the as.ab() and ab_* functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
You can add your own manual codes to be considered by as.ab() and all ab_* functions, see add_custom_antimicrobials().
add_custom_antimicrobials()
NA_ab_ is a missing value of the new ab class, analogous to e.g. base R's NA_character_.
ab
This is based on:
Lancefield RC (1933). A serological differentiation of human and other groups of hemolytic streptococci. J Exp Med. 57(4): 571-95; doi:10.1084/jem.57.4.571
NA_mo_ is a missing value of the new mo class, analogous to e.g. base R's NA_character_.
mo
as.mo()
is.mo()
mo_uncertainties()
mo_renamed()
mo_failures()
mo_reset_session()
mo_cleaning_regex()
is.ab()
ab_reset_session()