Compare phylogenetic structural equation models

Fits several phylogenetic structural equation model for further comparison

Usage

compare_phylosem(
  sem_set,
  tree,
  data,
  family = Map(function(.) fixed(), colnames(data)),
  covs,
  estimate_ou = FALSE,
  estimate_lambda = FALSE,
  estimate_kappa = FALSE,
  control = phylosem_control(),
  ...
)

Arguments

sem_set

A named list of structural equation model specifications, where each element will be passed as argument sem to phylosem

tree

phylogenetic structure, using class as.phylo

data

data-frame providing numeric values for variables being modeled. Missing values are inputted as NA. If an SEM includes a latent variable (i.e., variable with no available measurements) then it still must be inputted as a column of data with entirely NA values. Bernoulli variables must be coded as 0s or 1s, and factors are not allowed.

family

A named list of families, each returning a class family, including [fixed()], [gaussian()], [binomial()], [Gamma()], and [poisson()], with names that match levels of colnames(data) to allow different families by variable. Family [fixed()] specifies that states are known (i.e., measurements for that variable have no error). Other families allow users to supply a link function including `identity`, `log`, `logit`, or `cloglog`. For example family = list(y = binomial("logit"), x = fixed()) would specify logit-linked Bernoulli distribution for variable `data$y` and a fixed (no measurement error) distribution for `data$x`. For many variables, it is convenient to do e.g., family = Map(function(.) gaussian(), colnames(tsdata)) rather than writing them all manually.

covs

optional: a character vector of one or more elements, with each element giving a string of variable names, separated by commas. Variances and covariances among all variables in each such string are added to the model. For confirmatory factor analysis models specified via cfa, covs defaults to all of the factors in the model, thus specifying all variances and covariances among these factors. Warning: covs="x1, x2" and covs=c("x1", "x2") are not equivalent: covs="x1, x2" specifies the variance of x1, the variance of x2, and their covariance, while covs=c("x1", "x2") specifies the variance of x1 and the variance of x2 but not their covariance.

estimate_ou

Boolean indicating whether to estimate an autoregressive (Ornstein-Uhlenbeck) process using additional parameter lnalpha, corresponding to the model="OUrandomRoot" parameterization from phylolm as listed in doi:10.1093/sysbio/syu005

estimate_lambda

Boolean indicating whether to estimate additional branch lengths for phylogenetic tips (a.k.a. the Pagel-lambda term) using additional parameter logitlambda

estimate_kappa

Boolean indicating whether to estimate a nonlinear scaling of branch lengths (a.k.a. the Pagel-kappa term) using additional parameter lnkappa

control

Output from phylosem_control, used to define user settings, and see documentation for that function for details.

...

Additional arguments passed to phylosem

Value

An object (list) of class `compare_phylosem`, containing a list of output from phylosem