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clootl (version 0.1.2)

clootl_data: A complex data store used in the package.

Description

A dataset containing taxonomy files, summary phylogenies, constituent study information, and other data needed for the package to function properly.

Usage

clootl_data

Arguments

Format

List of csv files, phylogenies, and other data components.

Details

The data object, clootl_data, stores the most up-to-date stable version of the tree mapped to each of the different taxonomy years, the annotations of how each study contributed to the tree, the citation information for each study that contributed to the tree, the taxonomy crosswalks for different years, and some other variables.

The structure of the data store (a list) is as follows:

clootl_data$taxonomy.files

A list of data frames. Each element corresponds to a taxonomy year:

  • Year2024

  • Year2023

  • Year2022

  • Year2021

These originate as CSV files linking the Clements taxonomy for each of these years to OTT ids, Avibase ids, and other bird taxonomies (see README of https://github.com/McTavishLab/AvesData).

clootl_data$trees
summary.trees

Phylo objects of complete dated trees mapped to the Clements taxonomy year:

  • year2024

  • year2023

  • year2022

  • year2021

These are generated from summary_dated_clements.nex (see https://github.com/McTavishLab/AvesData README).

annotations

Complete annotations of the OpenTree synthetic tree for this version, used to determine appropriate subtree citations.

clootl_data$study_info

A mapping of OpenTree study ids to full citations. Used with annotations to generate appropriate citations for trees and subtrees.

clootl_data$versions

A character vector of all possible tree versions. To access older versions, download the data repository using get_avesdata_repo().

clootl_data$tax_years

A character vector of all available taxonomies. The current tree version is mapped to each of these taxonomies, along with crosswalks linking the Clements taxonomy for each year to other identifiers.

This data object is generated using the following code:


clootl_data = list()
clootl_data$versions <- c("1.2","1.3","1.4","1.5")
fullTree2021 <- treeGet("1.5","2021", data_path="~/projects/otapi/AvesData")
fullTree2022 <- treeGet("1.5","2022", data_path="~/projects/otapi/AvesData")
fullTree2023 <- treeGet("1.5","2023", data_path="~/projects/otapi/AvesData")
fullTree2024 <- treeGet("1.5","2024", data_path="~/projects/otapi/AvesData")
tax2021 <- taxonomyGet(2021, data_path="~/projects/otapi/AvesData")
tax2022 <- taxonomyGet(2022, data_path="~/projects/otapi/AvesData")
tax2023 <- taxonomyGet(2023, data_path="~/projects/otapi/AvesData")
tax2024 <- taxonomyGet(2024, data_path="~/projects/otapi/AvesData")
clootl_data$taxonomy.files$Year2021 <- tax2021
clootl_data$taxonomy.files$Year2022 <- tax2022
clootl_data$taxonomy.files$Year2023 <- tax2023
clootl_data$taxonomy.files$Year2024 <- tax2024
clootl_data$tax_years <- c("2021","2022","2023","2024")
annot_filename <- "~/projects/otapi/AvesData/Tree_versions/Aves_1.5/OpenTreeSynth/annotated_supertree/annotations.json"
all_nodes <- jsonlite::fromJSON(txt=annot_filename)
clootl_data$trees$Aves_1.5$annotations <- all_nodes
studies <- c()
for (inputs in all_nodes$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")