Nothing
utils::globalVariables(c("context", "sites"))
#' @import dplyr
#' @export
#' @title Extract taxonomic data from a set of sites.
#' @description From a sites object,
#' @param object A \code{sites} object.
#' @returns A \code{data.frame} reporting the taxa/data objects, units,
#' elements and other features within a set of records.
#' @examples \donttest{
#' somesites <- get_sites(datasettype = "diatom", limit = 3) %>%
#' get_downloads()
#' diatomtaxa <- taxa(somesites)
#' common_taxa <- diatomtaxa %>%
#' dplyr::filter(sites == 3)
#' }
#'
setMethod(f = "taxa",
signature = "sites",
definition = function(object) {
output <- purrr::map(object@sites, function(y) taxa(y)) %>%
dplyr::bind_rows() %>%
group_by(units,
context,
element,
taxonid,
symmetry,
taxongroup,
elementtype,
variablename,
ecologicalgroup) %>%
summarise(samples = sum(samples),
sites = sum(sites), .groups = "keep")
if(nrow(output) == 0){
warnsite <- sprintf("No assigned samples. Did you run get_downloads()?")
warning(warnsite)
}
return(output)
}
)
#' @title Extract taxonomic data from a single site.
#' @param object A \code{site} object.
#' @returns A \code{data.frame} reporting the taxa/data objects, units,
#' elements and other features within a set of records.
#' @examples \donttest{
#' somesites <- get_sites(datasettype = "pollen", limit = 3) %>%
#' get_downloads()
#' diatomtaxa <- taxa(somesites[[1]])
#' }
setMethod(f = "taxa",
signature = "site",
definition = function(object) {
samples <- samples(object)
tx_table <- samples %>%
group_by(units,
context,
element,
taxonid,
symmetry,
taxongroup,
elementtype,
variablename,
ecologicalgroup,
siteid) %>%
summarise(samples = n(), .groups = "keep") %>%
group_by(units,
context,
element,
taxonid,
symmetry,
taxongroup,
elementtype,
variablename,
ecologicalgroup) %>%
summarise(sites = n(), samples = sum(samples), .groups = "keep")
return(tx_table)
})
#' @title Extract taxonomic data from a set of sites.
#' @param object A \code{collunits} object.
#' @returns A \code{data.frame} reporting the taxa/data objects, units,
#' elements and other features within a set of records.
setMethod(f = "taxa",
signature = "collunits",
definition = function(object) {
samples <- samples(object)
tx_table <- samples %>%
group_by(units,
context,
element,
taxonid,
symmetry,
taxongroup,
elementtype,
variablename,
ecologicalgroup,
siteid) %>%
summarise(samples = n(), .groups = "keep") %>%
group_by(units,
context,
element,
taxonid,
symmetry,
taxongroup,
elementtype,
variablename,
ecologicalgroup) %>%
summarise(sites = n(), samples = sum(samples), .groups = "keep")
return(tx_table)
})
#' @title Extract taxonomic data from a set of sites.
#' @param object A \code{collunit} object.
#' @returns A \code{data.frame} reporting the taxa/data objects, units,
#' elements and other features within a set of records.
setMethod(f = "taxa",
signature = "collunit",
definition = function(object) {
samples <- samples(object)
tx_table <- samples %>%
group_by(units,
context,
element,
taxonid,
symmetry,
taxongroup,
elementtype,
variablename,
ecologicalgroup,
siteid) %>%
summarise(samples = n(), .groups = "keep") %>%
group_by(units,
context,
element,
taxonid,
symmetry,
taxongroup,
elementtype,
variablename,
ecologicalgroup) %>%
summarise(sites = n(), samples = sum(samples), .groups = "keep")
return(tx_table)
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.