Phylogeny Based Biodiversity Data Queries

# Phylogeny Based Biodiversity Data Queries

.center[
## Scott Chamberlain
### UC Berkeley - rOpenSci
<img src="img/icon_lettering_color.svg" alt="ropensci" width="600" />
]

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## [scotttalks.info/tdwg18](https://scotttalks.info/tdwg17)
 
## LICENSE: [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)
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# 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

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via <a href="https://www.bioconductor.org/packages/release/bioc/vignettes/ggtree/inst/doc/treeVisualization.html">ggtree tutorial</a>

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via <a href="http://api.gbif.org/v2/map/debug/">GBIF map API demos</a>

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lots of papers combining phylogenies and biodiversity

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# How do we quickly link the two?

## Ideally we want:

## users to be able to ask A LOT of questions VERY QUICKLY

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# phylodiv - an R package

## source code: [ropensci/phylodiv](https://github.com/ropensci/phylodiv)

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# phylodiv - an R package

## builds on top of ...

## - [taxizedb][] for taxonomy data
## - [rgbif][] for biodiversity data
## - [rgbif][]/[raster][]/[ggplot2][]/[ggtree][]/[patchwork][]/etc. for mapping

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# High level workflow

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

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# 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()
```

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# High level workflow

rapid iteration between phylogenetic queries and vizualization

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LIVE DEMO

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# this will be easy, right?

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# hard parts

## Taxonomic names 
## Queries on trees
## Biodiversity data
## Visualization

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# 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](https://github.com/ropensci/taxa/issues/184) for discussion)

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# 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

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# Queries

### formula syntax?

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

### function calls?

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

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# 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

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# 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`)

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# 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 😏

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# Future work

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# 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

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[rgbif]: https://github.com/ropensci/rgbif
[taxizedb]: https://github.com/ropensci/taxizedb
[taxa]: https://github.com/ropensci/taxa
[ggplot2]: https://github.com/tidyverse/ggplot2
[taxizedb]: https://github.com/ropensci/taxizedb
[patchwork]: https://github.com/thomasp85/patchwork
[ggtree]: https://www.bioconductor.org/packages/release/bioc/html/ggtree.html
[raster]: https://cran.r-project.org/package=raster
[phyloreferencing]: https://www.phyloref.org/
[spocc]: https://github.com/ropensci/spocc