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(v2.1.1.9279) fix documentation, add foreign S3 exports to functions

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dr. M.S. (Matthijs) Berends
2025-05-16 16:55:29 +02:00
parent 139f79d372
commit 38cebc1541
24 changed files with 292 additions and 239 deletions
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100
R/zzz.R
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@ -94,106 +94,6 @@ AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
.onLoad <- function(libname, pkgname) {
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
# without the need to depend on other packages. This was suggested by the
# developers of the vctrs package:
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
s3_register("pillar::pillar_shaft", "ab")
s3_register("pillar::pillar_shaft", "av")
s3_register("pillar::pillar_shaft", "mo")
s3_register("pillar::pillar_shaft", "sir")
s3_register("pillar::pillar_shaft", "mic")
s3_register("pillar::pillar_shaft", "disk")
# no type_sum of disk, that's now in vctrs::vec_ptype_full
s3_register("pillar::type_sum", "ab")
s3_register("pillar::type_sum", "av")
s3_register("pillar::type_sum", "mo")
s3_register("pillar::type_sum", "sir")
s3_register("pillar::type_sum", "mic")
s3_register("pillar::tbl_sum", "antibiogram")
s3_register("pillar::tbl_format_footer", "antibiogram")
# Support for frequency tables from the cleaner package
s3_register("cleaner::freq", "mo")
s3_register("cleaner::freq", "sir")
# Support for skim() from the skimr package
if (pkg_is_available("skimr", min_version = "2.0.0")) {
s3_register("skimr::get_skimmers", "mo")
s3_register("skimr::get_skimmers", "sir")
s3_register("skimr::get_skimmers", "mic")
s3_register("skimr::get_skimmers", "disk")
}
# Support for autoplot() from the ggplot2 package
s3_register("ggplot2::autoplot", "sir")
s3_register("ggplot2::autoplot", "mic")
s3_register("ggplot2::autoplot", "disk")
s3_register("ggplot2::autoplot", "resistance_predict")
s3_register("ggplot2::autoplot", "antibiogram")
# Support for fortify from the ggplot2 package
s3_register("ggplot2::fortify", "sir")
s3_register("ggplot2::fortify", "mic")
s3_register("ggplot2::fortify", "disk")
# Support for knitr (R Markdown/Quarto)
s3_register("knitr::knit_print", "antibiogram")
s3_register("knitr::knit_print", "formatted_bug_drug_combinations")
# Support vctrs package for use in e.g. dplyr verbs
# (NOTE 2024-02-22 this is the right way - it should be 2 '.'-separated S3 classes in the second argument)
# S3: amr_selector
s3_register("vctrs::vec_ptype2", "character.amr_selector")
s3_register("vctrs::vec_ptype2", "amr_selector.character")
s3_register("vctrs::vec_cast", "character.amr_selector")
# S3: amr_selector_any_all
s3_register("vctrs::vec_ptype2", "logical.amr_selector_any_all")
s3_register("vctrs::vec_ptype2", "amr_selector_any_all.logical")
s3_register("vctrs::vec_cast", "logical.amr_selector_any_all")
# S3: ab
s3_register("vctrs::vec_ptype2", "ab.default")
s3_register("vctrs::vec_ptype2", "ab.ab")
s3_register("vctrs::vec_cast", "character.ab")
s3_register("vctrs::vec_cast", "ab.character")
# S3: av
s3_register("vctrs::vec_ptype2", "av.default")
s3_register("vctrs::vec_ptype2", "av.av")
s3_register("vctrs::vec_cast", "character.av")
s3_register("vctrs::vec_cast", "av.character")
# S3: mo
s3_register("vctrs::vec_ptype2", "mo.default")
s3_register("vctrs::vec_ptype2", "mo.mo")
s3_register("vctrs::vec_cast", "character.mo")
s3_register("vctrs::vec_cast", "mo.character")
# S3: disk
s3_register("vctrs::vec_ptype_full", "disk")
s3_register("vctrs::vec_ptype_abbr", "disk")
s3_register("vctrs::vec_ptype2", "disk.default")
s3_register("vctrs::vec_ptype2", "disk.disk")
s3_register("vctrs::vec_cast", "disk.disk")
s3_register("vctrs::vec_cast", "integer.disk")
s3_register("vctrs::vec_cast", "disk.integer")
s3_register("vctrs::vec_cast", "double.disk")
s3_register("vctrs::vec_cast", "disk.double")
s3_register("vctrs::vec_cast", "character.disk")
s3_register("vctrs::vec_cast", "disk.character")
# S3: mic
s3_register("vctrs::vec_ptype2", "mic.default")
s3_register("vctrs::vec_ptype2", "mic.mic")
s3_register("vctrs::vec_cast", "character.mic")
s3_register("vctrs::vec_cast", "double.mic")
s3_register("vctrs::vec_cast", "integer.mic")
s3_register("vctrs::vec_cast", "factor.mic")
s3_register("vctrs::vec_cast", "mic.character")
s3_register("vctrs::vec_cast", "mic.double")
s3_register("vctrs::vec_cast", "mic.integer")
s3_register("vctrs::vec_cast", "mic.factor")
s3_register("vctrs::vec_cast", "mic.mic")
s3_register("vctrs::vec_math", "mic")
s3_register("vctrs::vec_arith", "mic")
# S3: sir
s3_register("vctrs::vec_ptype2", "sir.default")
s3_register("vctrs::vec_ptype2", "sir.sir")
s3_register("vctrs::vec_ptype2", "character.sir")
s3_register("vctrs::vec_cast", "character.sir")
s3_register("vctrs::vec_cast", "sir.character")
s3_register("vctrs::vec_cast", "sir.sir")
# if mo source exists, fire it up (see mo_source())
if (tryCatch(file.exists(getOption("AMR_mo_source", "~/mo_source.rds")), error = function(e) FALSE)) {
try(invisible(get_mo_source()), silent = TRUE)