clootl_data: A complex data store used in the package.

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

A complex data store used in the package.

Description

Taxonomy files and phylogenies.

Usage

clootl_data

Format

List of csv files and Newick and Nexus phylogenies

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")

Source

https://github.com/eliotmiller/clootl

clootl documentation built on April 11, 2025, 5:38 p.m.