*phytools* has a new version on CRAN (*phytools* 2.3-0). The previous CRAN version (2.1-1) was published in January, and I’ve been doing a lot since then, so this version has *many* new features and methods. Hopefully, I’ll get around to surveying some of these in the coming days.

The function I’m most excited about *right now*, however, is unambiguously `fitmultiBM`

for fitting a discrete character dependent multi-rate Brownian motion model to continuous trait data using the discrete approximation of Boucher & Démery (2016). I have already written about this method here, here, here, and here.

Today, before submitting the new *phytools* CRAN version, I first pushed a number of new updates to this function – to improve optimization (a bit – it’s still slow), to add ancestral state estimation under the model, and to create a visualization of the model structure.

I’m going to explore ancestral state estimation under this model with another post.

Here, I want to show a workflow of model comparison including visualization of the structure of the fitted model. Hopefully this will help users better understand how this method works.

```
library(phytools)
packageVersion("phytools")
```

```
## [1] '2.3.0'
```

To start with, I’m going to simulate a phylogeny and a total of four different characters.

My first character, `y1`

, is a two-state discrete character with levels `1`

and `2`

, that evolved on the tree under a continuous-time Markov chain (M*k*) model.

My second character, `x1`

, is a continuous trait that evolved via Brownian motion on the tree, but with a rate, \(\sigma^2\), that depends on the *level* of `y1`

such that \(\sigma_{1}^2 = 1.0\) and \(\sigma_{2}^2 = 20\).

My *third* character, `y2`

, is a second continuous trait that evolved via the same process as `y1`

, but with levels `A`

and `B`

.

Finally, my fourth trait, `x2`

, is a continuous trait that evolved via Brownian motion with a rate that depended on `y2`

such that \(\sigma_{A}^2 = 20\) and \(\sigma_{B}^2 = 1.0\).

```
## simulate our tree
phy<-pbtree(n=100,scale=1)
phy
```

```
##
## Phylogenetic tree with 100 tips and 99 internal nodes.
##
## Tip labels:
## t5, t59, t76, t77, t74, t75, ...
##
## Rooted; includes branch lengths.
```

```
## our transition matrix for both y1 and y2
Q<-matrix(c(-1,1,1,-1),2,2,
dimnames=list(1:2,1:2))
Q
```

```
## 1 2
## 1 -1 1
## 2 1 -1
```

```
## discrete character history for y1
t1<-sim.history(phy,Q)
```

```
## Done simulation(s).
```

```
## simulate y1 and x1
y1<-factor(getStates(t1,"tips"))
sig2_1<-setNames(c(1,20),levels(y1))
x1<-sim.rates(t1,sig2_1)
```

```
## update Q
colnames(Q)<-rownames(Q)<-c("A","B")
Q
```

```
## A B
## A -1 1
## B 1 -1
```

```
## discrete character history for y2
t2<-sim.history(phy,Q)
```

```
## Done simulation(s).
```

```
## simulate y2 and x2
y2<-factor(getStates(t2,"tips"))
sig2_2<-setNames(c(20,1),levels(y2))
x2<-sim.rates(t2,sig2_2)
```

To start off, I’ll focus on `x1`

and `y1`

and imagine that we had an *a priori* hypothesis that the state of `y1`

influenced the rate of `x1`

.

We can fit that model as follows.

```
sd_fit1<-fitmultiBM(phy,x1,y1,levs=100,
parallel=TRUE,plot_model=TRUE)
```

The way to understand the graph of our fitted model is that every square is a `levs`

\(\times\) `levs`

submatrix. Those on the diagonal describe continuous trait evolution *within* a regime, whereas non-diagonal submatrices give the transitions in the discrete trait *between* regimes. Each different color corresponds to a different parameter to be estimated in the model.

```
sd_fit1
```

```
## Object of class "fitmultiBM" based on
## a discretization with k = 100 levels.
##
## Fitted multi-rate BM model parameters:
## levels: [ 1, 2 ]
## sigsq: [ 0.9299, 16.3279 ]
## x0: -0.3036
##
## Estimated Q matrix:
## 1 2
## 1 -1.57855 1.57855
## 2 1.57855 -1.57855
##
## Log-likelihood: -206.8113
##
## R thinks it has found the ML solution.
```

We might recall that our generating rates were \(\sigma^2 = [1, 20]\) and think that we might be onto something here!

On the other hand, we haven’t asked how well a constant rate model explains our data. Let’s fit that model and compare.

```
cr_null1<-fitmultiBM(phy,x1,y1,levs=100,
parallel=TRUE,plot_model=TRUE,null_model=TRUE)
```

We can see that this is a null model because the continuous trait evolution within each of our two discrete character levels are *equal* one to the other, as indicated by the colors in our matrix!

```
cr_null1
```

```
## Object of class "fitmultiBM" based on
## a discretization with k = 100 levels.
##
## Fitted multi-rate BM model parameters:
## levels: [ 1, 2 ]
## sigsq: [ 8.0242, 8.0242 ]
## x0: 0.5535
##
## Estimated Q matrix:
## 1 2
## 1 -1.26584 1.26584
## 2 1.26584 -1.26584
##
## Log-likelihood: -238.1674
##
## R thinks it has found the ML solution.
```

It’s not hard to see that, compared to our state-dependent model, a constant-rates process does not explain our data very well!

There’s *another* “null” model, however, that might be worth considering – and that’s one in which our evolutionary rates varies according to some discrete trait, just not the one we measured! This is a type of hidden Markov model and we can fit that using `fitmultiBM`

too! Let’s try it.

```
hrm_null1<-fitmultiBM(phy,x1,y1,levs=100,
parallel=TRUE,plot_model=TRUE,null_model=TRUE,
ncat=2)
```

Once again, the reason I call this a “null” (with air-quotes) model is because the rate of continuous trait evolution, \(\sigma^2\), is equal between our two different levels of the discrete trait (`0`

and `1`

) and only differ as a function of our hidden character (with two levels as indicated by the presence or absence of the `*`

).

```
hrm_null1
```

```
## Object of class "fitmultiBM" based on
## a discretization with k = 100 levels.
##
## Fitted multi-rate BM model parameters:
## levels: [ 1, 1*, 2, 2* ]
## sigsq: [ 16.3279, 1.1006, 16.3279, 1.1006 ]
## x0: -0.0179
##
## Estimated Q matrix:
## 1 1* 2 2*
## 1 -2.477284 1.211444 1.265840 0.000000
## 1* 1.211444 -2.477284 0.000000 1.265840
## 2 1.265840 0.000000 -2.477284 1.211444
## 2* 0.000000 1.265840 1.211444 -2.477284
##
## Log-likelihood: -219.8385
##
## R thinks it has found the ML solution.
```

As far as I can tell, this hidden-rates model does not seem to explain our data nearly as well as our original state-dependent model.

One last model we can consider is one in which *both* our discrete character *and* a hidden character affect the rate of evolution of our continuous trait. This model has the *most* parameters and well take the most time to fit, so let’s not delay!

```
sd_fit1.hrm<-fitmultiBM(phy,x1,y1,levs=100,
parallel=TRUE,plot_model=TRUE,ncat=2)
```

```
sd_fit1.hrm
```

```
## Object of class "fitmultiBM" based on
## a discretization with k = 100 levels.
##
## Fitted multi-rate BM model parameters:
## levels: [ 1, 1*, 2, 2* ]
## sigsq: [ 1.0501, 0.9254, 1.47, 16.3279 ]
## x0: -0.3036
##
## Estimated Q matrix:
## 1 1* 2 2*
## 1 -1.62375085 0.04234617 1.58140468 0.00000000
## 1* 0.04234617 -1.62375085 0.00000000 1.58140468
## 2 1.58140468 0.00000000 -1.62375085 0.04234617
## 2* 0.00000000 1.58140468 0.04234617 -1.62375085
##
## Log-likelihood: -206.7758
##
## R thinks it has found the ML solution.
```

Once again, this model has a slightly higher log-likelihood (but just barely) compared to our original state-dependent model. This makes sense, because in our generating model `x1`

depended *only* on `y1`

and not on some unobserved factor.

Let’s pit all four models against each other.

```
anova(cr_null1,sd_fit1,hrm_null1,sd_fit1.hrm)
```

```
## log(L) d.f. AIC weight
## cr_null1 -238.1674 3 482.3348 0.000000
## sd_fit1 -206.8113 4 421.6226 0.950944
## hrm_null1 -219.8385 5 449.6770 0.000001
## sd_fit1.hrm -206.7758 7 427.5516 0.049056
```

This affirms our impression that `sd_fit1`

, our original state-dependent model, is best-supported for these data.

How about `x2`

and `y2`

?

Actually, the reason I simulated these data as well was so I could demonstrate what happens when our continuous trait *has* evolved in a discrete state-dependent fashion, just not in response to the trait we hypothesized.

To see that, let’s fit a model in which the rate of evolution of `x2`

depends not on `y2`

, but on `y1`

, then on a hidden character, then on both `y1`

and a hidden character, and compare the results. This time I’m going to start with our “null” models. (This time we won’t plot our models.)

```
## constant rate null model
cr_null2<-fitmultiBM(phy,x2,y1,levs=100,
parallel=TRUE,null_model=TRUE)
cr_null2
```

```
## Object of class "fitmultiBM" based on
## a discretization with k = 100 levels.
##
## Fitted multi-rate BM model parameters:
## levels: [ 1, 2 ]
## sigsq: [ 11.2695, 11.2695 ]
## x0: -0.1364
##
## Estimated Q matrix:
## 1 2
## 1 -1.265837 1.265837
## 2 1.265837 -1.265837
##
## Log-likelihood: -254.5506
##
## R thinks it has found the ML solution.
```

```
## hidden-state dependent null
hrm_null2<-fitmultiBM(phy,x2,y1,levs=100,
parallel=TRUE,null_model=TRUE,ncat=2)
hrm_null2
```

```
## Object of class "fitmultiBM" based on
## a discretization with k = 100 levels.
##
## Fitted multi-rate BM model parameters:
## levels: [ 1, 1*, 2, 2* ]
## sigsq: [ 16.6849, 0.9114, 16.6849, 0.9114 ]
## x0: 0.7301
##
## Estimated Q matrix:
## 1 1* 2 2*
## 1 -1.9760868 0.7102485 1.2658383 0.0000000
## 1* 0.7102485 -1.9760868 0.0000000 1.2658383
## 2 1.2658383 0.0000000 -1.9760868 0.7102485
## 2* 0.0000000 1.2658383 0.7102485 -1.9760868
##
## Log-likelihood: -227.4381
##
## R thinks it has found the ML solution.
```

```
## state-dependent model
sd_fit2<-fitmultiBM(phy,x2,y1,levs=100,
parallel=TRUE)
sd_fit2
```

```
## Object of class "fitmultiBM" based on
## a discretization with k = 100 levels.
##
## Fitted multi-rate BM model parameters:
## levels: [ 1, 2 ]
## sigsq: [ 16.6849, 1.0642 ]
## x0: 0.7301
##
## Estimated Q matrix:
## 1 2
## 1 -1.826309 1.826309
## 2 1.826309 -1.826309
##
## Log-likelihood: -247.6183
##
## R thinks it has found the ML solution.
```

```
## both hidden-state and character-dependent
sd_fit2.hrm<-fitmultiBM(phy,x2,y1,levs=100,
parallel=TRUE,ncat=2)
sd_fit2.hrm
```

```
## Object of class "fitmultiBM" based on
## a discretization with k = 100 levels.
##
## Fitted multi-rate BM model parameters:
## levels: [ 1, 1*, 2, 2* ]
## sigsq: [ 16.6849, 0.9176, 13.6104, 0.8812 ]
## x0: 0.7301
##
## Estimated Q matrix:
## 1 1* 2 2*
## 1 -1.973112 0.709367 1.263745 0.000000
## 1* 0.709367 -1.973112 0.000000 1.263745
## 2 1.263745 0.000000 -1.973112 0.709367
## 2* 0.000000 1.263745 0.709367 -1.973112
##
## Log-likelihood: -227.3413
##
## R thinks it has found the ML solution.
```

Let’s compare *this* set of models.

```
anova(cr_null2,sd_fit2,hrm_null2,sd_fit2.hrm)
```

```
## log(L) d.f. AIC weight
## cr_null2 -254.5506 3 515.1012 0.00000
## sd_fit2 -247.6183 4 503.2366 0.00000
## hrm_null2 -227.4381 5 464.8762 0.87025
## sd_fit2.hrm -227.3413 7 468.6826 0.12975
```

This time around we should see that our hidden-rates “null” model in which `x2`

evolves in a state-dependent variable-rate fashion, but just not in response to the observed discrete trait (`y1`

) is the best-supported in the set. That makes sense.

Let’s take a closer look at this model.

```
hrm_null2
```

```
## Object of class "fitmultiBM" based on
## a discretization with k = 100 levels.
##
## Fitted multi-rate BM model parameters:
## levels: [ 1, 1*, 2, 2* ]
## sigsq: [ 16.6849, 0.9114, 16.6849, 0.9114 ]
## x0: 0.7301
##
## Estimated Q matrix:
## 1 1* 2 2*
## 1 -1.9760868 0.7102485 1.2658383 0.0000000
## 1* 0.7102485 -1.9760868 0.0000000 1.2658383
## 2 1.2658383 0.0000000 -1.9760868 0.7102485
## 2* 0.0000000 1.2658383 0.7102485 -1.9760868
##
## Log-likelihood: -227.4381
##
## R thinks it has found the ML solution.
```

Remember that our generating values of \(\sigma^2\) were \([1,20]\) (though they won’t necessarily appear in that order, of course), and the transition rate between character levels for the (unobserved) discrete trait was \(q = 1.0\).

How did we do?

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