#' load_taxa
#'
#' @param server Either "fishbase" (the default) or "sealifebase"
#' @param version the version of the database you want. Will default to the
#' latest avialable; see [available_releases()].
#' @param db A remote database connection. Will default to the best available
#' system, see [default_db()].
#' @param collect return a data.frame if TRUE, otherwise, a DBI connection to
#' the table in the database
#' @param ... for compatibility with previous versions
#' @return the taxa list
#' @export
load_taxa <- function(server = getOption("FISHBASE_API", "fishbase"),
version = get_latest_release(),
db = default_db(server, version),
collect = TRUE,
...){
#db_tbl <- tbl_name("taxa", server, version)
#if(has_table(db_tbl)) return(dplyr::tbl(db, db_tbl))
## SeaLifeBase requires a different taxa table function:
if(is.null(server)) server <- getOption("FISHBASE_API", FISHBASE_API)
if(grepl("sealifebase", server)){
taxa_table <- slb_taxa_table(server, version, db)
} else {
taxa_table<- fb_taxa_table(server, version, db)
}
if(collect) return(dplyr::collect(taxa_table))
taxa_table
}
globalVariables(c("SpecCode", "Species", "Genus", "Subfamily", "Family",
"Order", "Class", "SuperClass", "Phylum", "Kingdom", "tempcolumn"))
fb_taxa_table <-
function(server = getOption("FISHBASE_API", "fishbase"),
version = get_latest_release(),
db = default_db(server, version)){
taxon_species <- fb_tbl("species", server, version, db) %>%
select("SpecCode", "Species", "Genus", "Subfamily",
"GenCode", "SubGenCode", "FamCode")
taxon_genus <- fb_tbl("genera", server, version, db) %>%
select("GenCode", "GenName", "GenusCommonName" = "GenComName",
"FamCode", "Subfamily", "SubgenusOf")
taxon_family <- fb_tbl("families", server, version, db) %>%
select("FamCode", "Family","FamilyCommonName" = "CommonName", "Order",
"Ordnum", "Class", "ClassNum")
taxon_order <- fb_tbl("orders", server, version, db) %>%
select("Ordnum", "Order", "OrderCommonName" = "CommonName",
"ClassNum", "Class")
taxon_class <- fb_tbl("classes", server, version, db) %>%
select("ClassNum", "Class", "ClassCommonName" = "CommonName",
"SuperClass", "Subclass")
taxon_hierarchy <-
taxon_species %>%
left_join(taxon_genus) %>%
left_join(taxon_family )%>%
left_join(taxon_order) %>%
left_join(taxon_class)
taxa_table <-
taxon_hierarchy %>%
dplyr::select("SpecCode", "Species", "Genus", "Subfamily", "Family",
"Order", "Class", "SuperClass") %>%
dplyr::mutate(Species = paste(Genus, Species)) %>%
dplyr::compute(temporary=FALSE)
taxa_table
}
slb_taxa_table <- function(server, version, db){
server <- "sealifebase"
taxon_species <- fb_tbl("species", server, version, db) %>%
select("SpecCode", "Species", "Genus",
"GenCode", "SubGenCode", "FamCode")
taxon_genus <- fb_tbl("genera", server, version, db) %>%
select("GenCode", "Genus" = "GEN_NAME", "GenusCommonName" = "CommonName", "FamCode" = "Famcode",
"Subfamily")
taxon_family <- fb_tbl("families", server, version, db) %>%
select("FamCode", "Family","FamilyCommonName"="CommonName", "Order",
"Ordnum", "Class", "ClassNum")
taxon_order <- fb_tbl("orders", server, version, db) %>%
select("Ordnum", "Order", "OrderCommonName"= "CommonName", "ClassNum", "Class")
taxon_class <- fb_tbl("classes", server, version, db) %>%
select("ClassNum", "Class", "ClassCommonName" = "CommonName")
taxon_phylum <- fb_tbl("phylums", server, version, db) %>%
select("PhylumId", "Phylum", "Kingdom", "PhylumCommonName" = "CommonName")
phylum_class <- fb_tbl("phylumclass", server, version, db)
suppressMessages(
taxon_hierarchy <-
taxon_species %>%
left_join(taxon_genus) %>%
left_join(taxon_family )%>%
left_join(taxon_order) %>%
left_join(taxon_class) %>%
left_join(phylum_class) %>%
left_join(taxon_phylum)
)
taxa_table <-
taxon_hierarchy %>%
dplyr::select("SpecCode", "Species", "Genus", "Subfamily", "Family",
"Order", "Class", "Phylum", "Kingdom") %>%
dplyr::mutate(Species = paste(Genus, Species)) #%>%
#dplyr::arrange("SpecCode")
taxa_table
}
#' A table of all the the species found in FishBase, including taxonomic
#' classification and the Species Code (SpecCode) by which the species is
#' identified in FishBase.
#'
#' @name fishbase
#' @docType data
#' @author Carl Boettiger \email{carl@@ropensci.org}
#' @keywords data
NULL
#' A table of all the the species found in SeaLifeBase, including taxonomic
#' classification and the Species Code (SpecCode) by which the species is
#' identified in SeaLifeBase
#'
#' @name sealifebase
#' @docType data
#' @author Carl Boettiger \email{carl@@ropensci.org}
#' @keywords data
NULL
## Code to update the package cache:
# fishbase <- load_taxa(update = TRUE, limit = 35000)
# sealifebase <- load_taxa(update=TRUE, server = "https://fishbase.ropensci.org/sealifebase", limit = 120000)
# save("fishbase", file = "data/fishbase.rda", compress = "xz")
# save("sealifebase", file = "data/sealifebase.rda", compress = "xz")
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