From b3fd55e1ffdbf779652cdaa05d2e350a81041619 Mon Sep 17 00:00:00 2001 From: Will Cornwell Date: Wed, 24 Apr 2024 15:34:50 +1000 Subject: [PATCH 1/3] removing hard cap on file size of current downloads. this is slower, but safer going forward --- R/load_taxonomic_resources.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/R/load_taxonomic_resources.R b/R/load_taxonomic_resources.R index 42cec041..01c77504 100644 --- a/R/load_taxonomic_resources.R +++ b/R/load_taxonomic_resources.R @@ -337,7 +337,6 @@ dataset_access_function <- tryCatch({ APC <- readr::read_csv( "https://biodiversity.org.au/nsl/services/export/taxonCsv", - n_max = 110000, col_types = readr::cols( .default = readr::col_character(), @@ -351,7 +350,6 @@ dataset_access_function <- APNI <- readr::read_csv( "https://biodiversity.org.au/nsl/services/export/namesCsv", - n_max = 140000, col_types = readr::cols( .default = readr::col_character(), From 4fe059cb39d3795563897741322db197a0c44d9b Mon Sep 17 00:00:00 2001 From: Will Cornwell Date: Wed, 24 Apr 2024 15:37:36 +1000 Subject: [PATCH 2/3] better wording in documentation --- R/native_anywhere_in_australia.R | 9 +++++---- man/native_anywhere_in_australia.Rd | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/R/native_anywhere_in_australia.R b/R/native_anywhere_in_australia.R index 05767c8b..bc0aff73 100644 --- a/R/native_anywhere_in_australia.R +++ b/R/native_anywhere_in_australia.R @@ -1,10 +1,11 @@ #' For a vector of taxon names in to the APC, check if the species are native anywhere in Australia #' -#' This function checks if the given species is native anywhere in Australia according to the APC. -#' Note that this will not detect within-Australia introductions, e.g. if a species is from Western Australia and is invasive on the east coast. -#' And recent invasions are unlikely to be documented yet in APC. +#' This function checks which species from a list is thought to be native anywhere in Australia according to the APC. +#' Important caveats: this will not detect within-Australia introductions, e.g. if a species is from Western Australia and is invasive on the east coast. +#' Also, very recent invasions are unlikely to be documented yet in APC. +#' Ideally check spelling and taxonomy updates first via \link{create_taxonomic_update_lookup}. #' For the complete matrix of species by states that also represents within-Australia invasions, -#' use \link{create_species_state_origin_matrix}. For spelling checks and taxonomy updates please see \link{create_taxonomic_update_lookup}. +#' use \link{create_species_state_origin_matrix}. #' #' @family diversity methods #' @param species A character string typically representing the binomial for the species. diff --git a/man/native_anywhere_in_australia.Rd b/man/native_anywhere_in_australia.Rd index 2e9e6cd4..537d4b28 100644 --- a/man/native_anywhere_in_australia.Rd +++ b/man/native_anywhere_in_australia.Rd @@ -17,11 +17,12 @@ A tibble with two columns: \code{species}, which is the same as the unique value and \code{native_anywhere_in_aus}, a vector indicating whether each species is native anywhere in Australia, introduced by humans from elsewhere, or unknown with respect to the APC resource. } \description{ -This function checks if the given species is native anywhere in Australia according to the APC. -Note that this will not detect within-Australia introductions, e.g. if a species is from Western Australia and is invasive on the east coast. -And recent invasions are unlikely to be documented yet in APC. +This function checks which species from a list is thought to be native anywhere in Australia according to the APC. +Important caveats: this will not detect within-Australia introductions, e.g. if a species is from Western Australia and is invasive on the east coast. +Also, very recent invasions are unlikely to be documented yet in APC. +Ideally check spelling and taxonomy updates first via \link{create_taxonomic_update_lookup}. For the complete matrix of species by states that also represents within-Australia invasions, -use \link{create_species_state_origin_matrix}. For spelling checks and taxonomy updates please see \link{create_taxonomic_update_lookup}. +use \link{create_species_state_origin_matrix}. } \examples{ \donttest{native_anywhere_in_australia(c("Eucalyptus globulus","Pinus radiata","Banksis notaspecies"))} From 18171652101bad43f4da0913bac3bab425e766e3 Mon Sep 17 00:00:00 2001 From: Will Cornwell Date: Wed, 24 Apr 2024 15:41:58 +1000 Subject: [PATCH 3/3] other place there was a hard cap --- R/release.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/R/release.R b/R/release.R index cc071d33..76297bbf 100644 --- a/R/release.R +++ b/R/release.R @@ -23,7 +23,6 @@ download_taxonomic_resources_for_release<- function(version_name = NULL, path = APC <- readr::read_csv( "https://biodiversity.org.au/nsl/services/export/taxonCsv", - n_max = 110000, col_types = readr::cols( .default = readr::col_character(), @@ -43,7 +42,6 @@ readr::write_csv(APC, file = paste0(path,"apc.tar.gz")) APNI <- readr::read_csv( "https://biodiversity.org.au/nsl/services/export/namesCsv", - n_max = 140000, col_types = readr::cols( .default = readr::col_character(),