phylopath.Rmd

---
title: "Detailed comparison with `phylopath`"
author: "Wouter van der Bijl"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Detailed comparison with `phylopath`}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteDepends{phylopath,adephylo}
editor_options:
  chunk_output_type: console
---

```{r, include = FALSE}
have_packages = all(sapply( c("phylopath"), FUN=requireNamespace))
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = have_packages  # https://r-pkgs.org/vignettes.html#sec-vignettes-eval-option
)
# To isntall
#   devtools::install_local( R'(C:\Users\James.Thorson\Desktop\Git\phylosem)', force=TRUE )
# Test build:
#  setwd( R'(C:\Users\James.Thorson\Desktop\Git\phylosem\vignettes)' ); devtools::build_rmd( R'(vignettes\phylopath.Rmd)' )
# Render example
#  library(rmarkdown); setwd( R'(C:\Users\James.Thorson\Desktop\Git\phylosem\vignettes)' ); render( "phylopath.Rmd", pdf_document())
```

[_phylopath_](https://doi.org/10.7717/peerj.4718) is a package that implements phylogentic path analysis, using the d-separation methodology described by [Von Hardenberg & Gonzalez-Voyer](https://doi.org/10.1111/j.1558-5646.2012.01790.x). The models that can be fit are essentially a subset of the models that can be fit using _phylosem_. This is a comparison between the two packages, based on the introduction vignette of _phylopath_, showing where the packages are similar and where they differ. This should also be useful for _phylopath_ users, that want to do the same kinds of analysis in _phylosem_.

To clearly show from which package each function originates, I'll use the `package::function` notation. Make sure you have both packages installed.

### Model comparison: some important differences

Let's start by loading the Rhinogrades example data and phylogeny. 

```{r package_warning, include=isFALSE(have_packages)}
print("Must install ggplot2, phylopath, phylolm, ape")
```

```{r setup}
data(rhino, rhino_tree, package = 'phylopath')
```

When we supply the data to the model comparison functions, there is already two important differences to flag here.

Firstly, `phylo_path` only consciders the columns of the data that are actually used in the models. But `compare_phylosem` does not. In `rhino`, our first column contains a copy of the species names, and so we need to exclude this column (using `rhino[-1]`). So, when using _phylosem_, make sure your data.frame contains only the variables you'd like to inlcude in the analysis.

Secondly, to get standardized path coefficients, _phylopath_ will standardize the data so that each variable has unit variance, but _phylosem_ keeps data on their original scale. To make a better comparison between the packages, I'll standardize the data manually here.

```{r}
rhino_std <- rhino[-1]
rhino_std[] <- lapply(rhino_std, scale)
```

Now we can define what causal models we want to compare. First in `phylopath`, we use formulas and can use `DAG()` to define a model, or `define_model_set()` to create a list of models:

```{r}
models_pp <- phylopath::define_model_set(
  one   = c(RS ~ DD),
  two   = c(DD ~ NL, RS ~ LS + DD),
  three = c(RS ~ NL),
  four  = c(RS ~ BM + NL),
  five  = c(RS ~ BM + NL + DD),
  six   = c(NL ~ RS, RS ~ BM),
  seven = c(NL ~ RS, RS ~ LS + BM),
  eight = c(NL ~ RS),
  nine  = c(NL ~ RS, RS ~ LS),
  .common = c(LS ~ BM, NL ~ BM, DD ~ NL)
)
```

In `phylosem`, we can define the models similarly, but need to use strings instead. Also note that we need to write out the parameter in front of each varialble (e.g. `b1`, `b2`, etc.). To compare multiple models, we collect all the models in a `list`:

```{r}
models_ps <- list(
  one   = 'RS = b1 * DD',
  two   = 'DD = b1 * NL; RS = b2 * LS + b3 * DD',
  three = 'RS = b1 * NL',
  four  = 'RS = b * BM + b2 * NL',
  five  = 'RS = b1 * BM + b2 * NL + b3 * DD',
  six   = 'NL = b1 * RS; RS = b2 * BM',
  seven = 'NL = b1 * RS; RS = b2 * LS + b3 * BM',
  eight = 'NL = b1 * RS',
  nine  = 'NL = b1 * RS; RS = b2 * LS'
)
# we add the .common paths, by pasting them at the end of each of the model strings, e.g.:
models_ps <- lapply(
  models_ps, 
  \(x) paste(x, c('LS = b1_ * BM; NL = b2_ * BM; DD = b3_ * NL'), sep = '; ')
)
```

We can now run the model comparison. _phylopath_ will use d-separation here, while _phylosem_ is fitting each structural equation model itself.

Note that for `phylo_path`, we specify here that we want the Brownian motion model (`"BM"`), which is the default for `compare_phylosem`.

```{r, eval=have_packages, results=FALSE, message=FALSE}
result_pp <- phylopath::phylo_path(
  models_pp, data = rhino_std, tree = rhino_tree, model = 'BM'
)

library(phylosem)
result_ps <- phylosem::compare_phylosem(
  models_ps, tree = rhino_tree, data = rhino_std
)
```

How did our models perform? For _phylopath_ we can use `summary` to get a table with CICc values:

```{r}
summary(result_pp)
```

For _phylosem_, we can extract the AIC values for each model:

```{r}
sapply(result_ps, AIC) |> sort()
```

Even though the methodology used is quite different, we do obtain a similar result: model 5 fits much better than the other models.

However, the methods do somewhat differ in the ranking of the other models. This is largely due to the different philosophies of the two approaches. _phylopath_ uses the PPA method as described by Von Hardenberg & Gonzalez-Voyer, which uses Shipley's d-separation. In essence, this method finds pairs of variables that a causal model claims are independent (or conditionally independent), and then tests whether that is indeed the case. _phylosem_ on the other hand directly evaluates the fit of the casual model to the data. So in a sense, _phylosem_ analyzes the paths included in the model while _phylopath_ analyzes the paths that are not included.

Another source of difference is that the CICc metric used by _phylopath_ employs a correction for small sample sizes that the _phylosem_'s AIC metric does not.

In conclusion, in cases where one model clearly fits best (and under a Brownian motion model) I would expect the methods to lead to the same conclusion, but don't expect model comparison results to match closely.

### Model fitting: sometimes different

To take the best model, a particular model, or to perform model averaging, _phylopath_ and _phylosem_ work largely in the same way. Both packages have implemented the `best()`, `choice()` and `average()` methods for their respective output types.

We can get the best model (model 5) using `best()`. For _phylopath_ the paths are now fitted, for _phylosem_ this has already been done and the model is just extracted from the `compare_phylosem` object:

```{r}
best_pp <- phylopath::best(result_pp)
best_ps <- phylosem::best(result_ps)
```

To compare the two, we can convert the _phylosem_ result in to the DAG format that _phylopath_ uses, and use the included plot functionality:

```{r, eval=have_packages, fig.dim = c(6, 6), out.width = "50%"}
plot(best_pp)
plot(as_fitted_DAG(best_ps))
```

_phylopath_ is now actually fitting the causal model itself, not performing the d-separation procedure. Because this makes the methods much more closely aligned, we can see that the output matches very closely.

However, this will generally only hold true when assuming Brownian motion. If we deviate from that assumption by using (as an example) Pagel's lambda model, which is the default in _phylopath_, this is no longer true:

```{r, eval=have_packages, results=FALSE, message=FALSE, fig.dim = c(6, 6), out.width = "50%"}
phylopath::est_DAG(
  models_pp$five, data = rhino_std, tree = rhino_tree, model = 'lambda'
) |> plot()
phylosem::phylosem(
  models_ps$five, tree = rhino_tree, data = rhino_std, estimate_lambda = TRUE
) |> as_fitted_DAG() |> plot()
```

The reason this happens is that _phylosem_ implements these additional parameters by estimating them as a single estimated parameter for the all variables in the model. _phylopath_, on the other hand, estimates a separate lambda on the residuals of each regression ran. For `est_DAG()` this means one lambda for each variable with a modelled cause, and for `phylo_path()` this means one lambda for each tested d-separation statement.