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README.md

Phenomap

Phenomap is an approach to present the current knowledge available In the Phenoscape Knowledgebase. It connects the available phenotypic information with specimens from IDigBio and plots them in various ways to show the availability of knowledge and how it is distributed. This allows also to visualize where there are gaps in our knowledge.

Currently, this is a demo mode. First, taxa need to be selected and then a trait associated with them. The main part of the app shows three plots. The map presents the distribution of available specimens from IdigBio. The bar charts represent the range of specimens available based on genus level followed by the different traits and the trait value associated with it. The phylogeny is based on the current Open Tree of Life for the taxa available with their plotted trait values at the tips.

For the future we aim to expand the shiny app in various ways. The app will hopefully presented on the Phenoscape Knowledgebase to give users the possibility to easily explore what is available. The selection of taxa and traits, as well as the connection to IDigBio is currently based on static files. We want to implement API queries to keep it up to date. Instead of selecting a taxon first, it shall be possible to select the trait first. The information of what is available will be expanded in general. It would be nice to present the distribution range of the taxa in comparison to the specimen data, which will allow to compare the sampling of the species to the range. Based on the species there shall be hyper links to the IDigBio specimens and information where the specimens can be found in case people want to further analyze the data.

Requirements

install.packages("shiny") install.packages("tidyverse") install.packages("maps") install.packages("cowplot") install.packages("rotl")

Set working directory to the /phenomap directory if it is not already. The data files are loaded as "data/".