What is rOpenSci?

* non-profit

* make open-source software for R

* software review

* community developers/users

* target science use cases

* staff communicating btw. scientists/data provders

phylodiv - an R package

source code: ropensci/phylodiv

phylodiv - an R package

builds on top of ...

- taxizedb for taxonomy data

- rgbif for biodiversity data

- rgbif/raster/ggplot2/ggtree/patchwork/etc. for mapping

High level workflow

read phylogeny
  gather higher taxonomy
    phylogenetic query
      gather biodiversity data
        visualization
... history

High level workflow

read phylogeny -> pd_read()
  gather higher taxonomy -> pd_taxa()
    phylogenetic query -> pd_query()
      gather biodiversity data -> pd_biodiv()
        visualization -> pd_viz()
... history -> pd_meta()

High level workflow

read phylogeny -> pd_read()
  gather higher taxonomy -> pd_taxa()
    phylogenetic query -> pd_query()
      gather biodiversity data -> pd_biodiv()
        visualization -> pd_viz()
... history -> pd_meta()

rapid iteration between phylogenetic queries and vizualization

hard parts

Taxonomic names

Queries on trees

Biodiversity data

Visualization

Taxonomy

* web or local data access (local faster, but requires more setup 😬)

* can we label nodes programatically?

• just talked to Emily yesterday 😮 ¿annotate via OpenTree of Life?

* higher taxonomic names on taxa w/o names?

* leverage taxa internally? (see ropensci/taxa#184 for discussion)

Queries

* how do we make queries on trees drop dead simple AND flexible

• all tips within node A
• node A vs. node B
• node A vs. node B and node C
• node A of tree 1 vs. node C of tree 2
• node D of each of 100 trees (bla! how do you viz. that?)
• Helianthus annuus vs. Helianthus angustifolius
• all names starting with Helianthus
• compare sub trees that match shape X

Queries

formula syntax?

A ~ .
A ~ B
A ~ B + C
t1.A ~ t2.C
D ~ t*

function calls?

descendants(A)
children(A) ~ descendants(Y)
tip(A) ~ tip(B)
tips(Helianthus*)
tip(A, tree = 1) ~ tip(W, tree = 78)

Biodiversity

* many levels of data

• total counts
• total counts faceted by variable (e.g., country)
• complete occurrence data
• visually summarized data (rasters)

* strike balance btw bringing as much data to bear on problem as possible & speed

* making dealing with web requests easier: rate limits, caching, etc.

* consistent queries across data sources: spocc already done hard work - may integrate

Maps

* how best to do visualizations for single trees vs. many trees

* so many customizations possible - can only give a very simplified subset + hopefully allowing customizations on top of (easy-ish with ggplot2/ggtree)

What do you want to see?

* is phylodiv a bad or good idea?

* what are your main pain points in linking phylogenies to biodiversity data?

* do you really need a GUI interface? or is a programmatic interface okay? is it worth it if you get greater reproducibility

* data sources: which ones do you trust? not everyone is likely to trust the same source 😏

Future work

Future work

Future work

* focus on ease of use first, performance later

* make more taxonomic databases work locally

* make queries easy

* can phyloreferencing help at all here?

* maybe break up into a few pkgs