Fits several phylogenetic structural equation model for further comparison
Usage
compare_phylosem(
sem_set,
tree,
data,
family = rep("fixed", ncol(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
tophylosem
- tree
phylogenetic structure, using class
as.phylo
- data
data-frame providing 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.- family
Character-vector listing the distribution used for each column of
data
, where each element must befixed
,normal
,binomial
, orpoisson
.family="fixed"
is default behavior and assumes that a given variable is measured exactly. Other options correspond to different specifications of measurement error.- 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"
andcovs=c("x1", "x2")
are not equivalent:covs="x1, x2"
specifies the variance ofx1
, the variance ofx2
, and their covariance, whilecovs=c("x1", "x2")
specifies the variance ofx1
and the variance ofx2
but not their covariance.- estimate_ou
Boolean indicating whether to estimate an autoregressive (Ornstein-Uhlenbeck) process using additional parameter
lnalpha
, corresponding to themodel="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