From 9389ce66d077d543f6e1a67919de3bff81da9bf9 Mon Sep 17 00:00:00 2001 From: Will Cornwell Date: Wed, 16 Oct 2024 11:24:29 +1100 Subject: [PATCH 1/2] fixing quiet option --- R/create_taxonomic_update_lookup.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/create_taxonomic_update_lookup.R b/R/create_taxonomic_update_lookup.R index b9444913..b4cc7bf7 100644 --- a/R/create_taxonomic_update_lookup.R +++ b/R/create_taxonomic_update_lookup.R @@ -167,7 +167,7 @@ create_taxonomic_update_lookup <- function(taxa, APNI_matches = TRUE, imprecise_fuzzy_matches = FALSE, identifier = NA_character_, - resources = load_taxonomic_resources(), + resources = load_taxonomic_resources(quiet = quiet), quiet = FALSE, output = NULL) { From d849a6831832a04a2e0c0b1125480f08e22377e7 Mon Sep 17 00:00:00 2001 From: Will Cornwell Date: Wed, 16 Oct 2024 11:46:51 +1100 Subject: [PATCH 2/2] updating docs --- DESCRIPTION | 4 ++-- R/create_taxonomic_update_lookup.R | 2 +- man/create_taxonomic_update_lookup.Rd | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 58447698..41b2d0d0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: APCalign Title: Resolving Plant Taxon Names Using the Australian Plant Census -Version: 1.1.0 +Version: 1.1.1 Authors@R: c( person(given = "Daniel", family = "Falster", role = c("aut", "cre", "cph"), email = "daniel.falster@unsw.edu.au", comment = c(ORCID = "0000-0002-9814-092X")), person(given = "Elizabeth", family = "Wenk", role = c("aut", "ctb"), email = "e.wenk@unsw.edu.au", comment = c(ORCID = "0000-0001-5640-5910")), @@ -38,7 +38,7 @@ Suggests: here, testthat (>= 3.0.0) Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Config/testthat/edition: 3 VignetteBuilder: knitr URL: https://traitecoevo.github.io/APCalign/, https://github.com/traitecoevo/APCalign diff --git a/R/create_taxonomic_update_lookup.R b/R/create_taxonomic_update_lookup.R index b4cc7bf7..09d02cd0 100644 --- a/R/create_taxonomic_update_lookup.R +++ b/R/create_taxonomic_update_lookup.R @@ -73,7 +73,7 @@ #' makes erroneous matches. #' @param identifier A dataset, location or other identifier, #' which defaults to NA. -#' @param quiet Logical to indicate whether to display messages while +#' @param quiet Logical to indicate whether to display messages while loading data and #' aligning taxa. #' @param output file path to save the output. If this file already exists, #' this function will check if it's a subset of the species passed in and try diff --git a/man/create_taxonomic_update_lookup.Rd b/man/create_taxonomic_update_lookup.Rd index e3ae8743..204bba1b 100644 --- a/man/create_taxonomic_update_lookup.Rd +++ b/man/create_taxonomic_update_lookup.Rd @@ -17,7 +17,7 @@ create_taxonomic_update_lookup( APNI_matches = TRUE, imprecise_fuzzy_matches = FALSE, identifier = NA_character_, - resources = load_taxonomic_resources(), + resources = load_taxonomic_resources(quiet = quiet), quiet = FALSE, output = NULL ) @@ -70,7 +70,7 @@ will default to loading them from a local place on your computer. If this is to be called repeatedly, it's much faster to load the resources using \code{\link{load_taxonomic_resources}} separately and pass the data in.} -\item{quiet}{Logical to indicate whether to display messages while +\item{quiet}{Logical to indicate whether to display messages while loading data and aligning taxa.} \item{output}{file path to save the output. If this file already exists,