R/data.R

In clootl: Fetch and Explore the Cornell Lab of Ornithology Open Tree of Life Avian Phylogeny

#' A complex data store used in the package.
#'
#' Taxonomy files and phylogenies.
#'
#' @format List of csv files and Newick and Nexus phylogenies
#' @source \url{https://github.com/eliotmiller/clootl}
#' @details
#' clootl_data = list()
#'
#' fullTree2021 <- treeGet("1.4","2021", data_path="~/projects/otapi/AvesData")
#' fullTree2022 <- treeGet("1.4","2022", data_path="~/projects/otapi/AvesData")
#' fullTree2023 <- treeGet("1.4","2023", data_path="~/projects/otapi/AvesData")
#' clootl_data$trees$`Aves_1.4`$summary.trees$year2021 <- fullTree2021
#' clootl_data$trees$`Aves_1.4`$summary.trees$year2022 <- fullTree2022
#' clootl_data$trees$`Aves_1.4`$summary.trees$year2023 <- fullTree2023
#'
#' clootl_data$versions <- c('1.2','1.3','1.4')
#
#' tax2021 <- taxonomyGet(2021, data_path="~/projects/otapi/AvesData")
#' tax2022 <- taxonomyGet(2022, data_path="~/projects/otapi/AvesData")
#' tax2023 <- taxonomyGet(2023, data_path="~/projects/otapi/AvesData")
#'
#' clootl_data$taxonomy.files$Year2021 <- tax2021
#' clootl_data$taxonomy.files$Year2022 <- tax2022
#' clootl_data$taxonomy.files$Year2023 <- tax2023
#'
#' clootl_data$tax_years <- c("2021","2022","2023")
#' annot_filename <- "~/projects/otapi/AvesData/Tree_versions/Aves_1.4/OpenTreeSynth/annotated_supertree/annotations.json"
#' all_nodes <- jsonlite::fromJSON(txt=annot_filename)
#'
#' clootl_data$trees$`Aves_1.4`$annotations <- all_nodes
#'
#' This part pre-processes all citations for studies in the tree
#' so we don't need to do any API calls later.
#' studies <-c()
#' for (inputs in all_nodes$source_id_map) studies<-c(studies, inputs$study_id)
#' studies <- unique(studies)
#' study_info <- clootl:::api_studies_lookup(studies)
#'
#' clootl_data$study_info <- study_info
#' save(clootl_data, file="~/projects/otapi/clootl/data/clootl_data.rda", compress="xz")
#'
"clootl_data"