Phase II: Using Our Toolbox

class: center, middle, inverse, title-slide

.title[
# Phase II: Using Our Toolbox
]
.subtitle[
## Module 5: SHARK!
]
.author[
### Dr. Christopher Kenaley
]
.institute[
### Boston College
]
.date[
### 2024/10/16
]

---

class: inverse, top
# In class today

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

.pull-left[
Today we'll ....

- Review WCR7

- Compare evolutionary rates

- Break down parallel processing

]

.pull-right[
![](https://upload.wikimedia.org/wikipedia/commons/thumb/3/3c/Full_Shot_of_a_Caribbean_Reef_Shark_at_Tiger_Beach_Bahamas.jpg/1600px-Full_Shot_of_a_Caribbean_Reef_Shark_at_Tiger_Beach_Bahamas.jpg)
]

---
class: inverse, top

## WCR7

.pull-left[

- To R studio

]

---
class: inverse, top
## Morphological disparity

.pull-left[

Do groups evolve at similar rates?
  
 `compare.evol.rates()`
 
- estimated as net rates of Procrustes shape evolution:
  - Brownian motion model
  - GPA aligned data (`A`)
  - names groups vector (`gp`)
  - phylogeny (`phy`)
  - outputs ratio
  
]

``` r
phy <- readNexus("shark_trees.nex")
phy2 <- keep.tip(phy,PCA$sp)
gp_hab <- PCA$habitat
names(gp_hab) <- PCA$sp
er <- compare.evol.rates(
  A=ldk_al$coords, 
  phy=phy2[[1]], 
  method="simulation",
  gp=gp_hab)
}
```

---
class: inverse, top
## Sloooooow

.pull-left[

comparative analyses can be really slow!
  
- we have ~200 sp
- 500 different trees to consider

.pull-right[

![](https://bcorgbio.github.io/class/mod5_proj_files/figure-html/timescale-1.png)

]

---
class: inverse, top
## Let's go parallel

Many options for parallel in r
  
- `doParallel`
- `parallel`*

allows processing with multiple cores
  - run a function in embarrasingly parallel way with `mcapply()`

``` r
my_fun <- function(x) {
    for (i in x) rnorm(1e+07)
}
t_nomc <- system.time(lapply(1:30, my_fun))
t_mc <- system.time(mclapply(1:30, my_fun,
    mc.cores = detectCores() - 2))  #8 cores
print(rbind(t_nomc, t_mc))
```

```
##        user.self sys.self elapsed user.child sys.child
## t_nomc     7.823    0.182   8.182      0.000      0.00
## t_mc       0.003    0.010   1.456      6.515      0.57
```

---
class: inverse, top
## Let's go parallel

allows processing with multiple cores
  - Need a custom function that receives `X`
  - What should `X` be?

``` r
er_fun <- function(x) {
    er <- compare.evol.rates(A = ldk_al$coords,
        phy = x, method = "simulation", gp = gp_hab)
}

er_l <- mclapply(phy2[1:2], er_fun, mc.cores = detectCores() -
    2)
```