The Whiz and Viz Bang of Data

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.title[
# The Whiz and Viz Bang of Data
]
.subtitle[
## The Basics of Visualizaiton and Modeling (part deux)
]
.author[
### Dr. Christopher Kenaley
]
.institute[
### Boston College
]
.date[
### 2025/9/17
]

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# In class today

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.14.0/css/all.min.css">

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Today we'll ....

- More on trees.

- Trees as input in models.

- Questions/Answers Module 3 project.

]

.pull-right[
![](https://www.nature.com/scitable/content/33796/Baum1_F8_FULL.jpg)
]

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# Trees: hard problems
.pull-left[
Estimating relationships/Making trees is hard!!

For 30 species . . .

`\(5 \cdot 10^{38}\)` possible unique topologies

- More solutions/topologies than stars in universe.

- NP complete: a class of problems that are the most computationally difficult in the world.

]

.pull-right[
![](3140_f25_9-19_files/figure-html/unnamed-chunk-2-1.png)
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# Trees: storing tree information

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Even hard to represent tree information

Newick format:

"(Bovine:0.69395,((Gibbon: 0.36079,((Orang: 0.33636,(Gorilla:0.17147,(Chimp: 0.19268, Human:0.11927): 0.08386): 0.06124) :0.15057): 0.54939),Mouse: 1.21460));"

![](https://media-cdn.tripadvisor.com/media/photo-s/14/b7/41/6d/front-view-of-newick.jpg)

]

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``` r
tre <- "(Bovine:0.69395,((Gibbon:0.36079,((Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268, Human:0.11927):0.08386):0.06124):0.15057):0.54939),Mouse:1.21460));
"

phy <- read.tree(text=tre)

plot(phy)
```

![](3140_f25_9-19_files/figure-html/unnamed-chunk-3-1.png)
]

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### Brownian motion
![](3140_f25_9-19_files/figure-html/unnamed-chunk-4-1.png)

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### Brownian motion
<center>

`\(V_{ij}= \gamma \times t_a\)`

Variation-covariation matrix, e.g. `ape::corBrownian()`