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mirror of https://github.com/msberends/AMR.git synced 2025-07-12 17:41:50 +02:00

(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update

This commit is contained in:
2024-07-16 14:51:57 +02:00
parent 4f9db23684
commit 640888f408
191 changed files with 321091 additions and 89382 deletions

11
R/zzz.R
View File

@ -6,9 +6,9 @@
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
@ -81,11 +81,12 @@ AMR_env$is_dark_theme <- NULL
AMR_env$chmatch <- import_fn("chmatch", "data.table", error_on_fail = FALSE)
AMR_env$chin <- import_fn("%chin%", "data.table", error_on_fail = FALSE)
# take cli symbols if available
# take cli symbols and error function if available
AMR_env$info_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$info %or% "i"
AMR_env$bullet_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$bullet %or% "*"
AMR_env$dots <- import_fn("symbol", "cli", error_on_fail = FALSE)$ellipsis %or% "..."
AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %or% "*"
AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
.onLoad <- function(lib, pkg) {
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
@ -104,6 +105,8 @@ AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %o
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")