partialprune <- function(
x, # Model
alpha = 0.01, # Significance
matrices, # Automatically chosen
verbose,
combinefun = unionmodel,
...){
# Verbose:
if (missing(verbose)){
verbose <- x@verbose
}
fixed <- NULL
mi_free <- NULL
# Matrices:
if (missing(matrices)){
if (x@model == "varcov"){
if (x@submodel == "ggm"){
matrices <- "omega"
} else if (x@submodel == "prec"){
matrices <- "kappa"
} else if (x@submodel == "chol"){
matrices <- "lowertri"
} else if (x@submodel == "cov"){
matrices <- "sigma"
}
} else if (x@model == "meta_varcov"){
matrices <- character(0)
if (x@types$y == "ggm"){
matrices <- c(matrices,"omega_y")
} else if (x@types$y == "prec"){
matrices <- c(matrices,"kappa_y")
}
# Random effects:
if (x@types$randomEffects == "ggm"){
matrices <- c(matrices,"omega_randomEffects")
} else if (x@types$randomEffects == "prec"){
matrices <- c(matrices,"kappa_randomEffects")
}
} else if (x@model == "lvm"){
# Only add GGM structures to search:
matrices <- character(0)
if (x@types$latent == "ggm"){
matrices <- c(matrices,"omega_zeta")
} else if (x@types$latent == "prec"){
matrices <- c(matrices,"kappa_zeta")
}
if (x@types$residual == "ggm"){
matrices <- c(matrices,"omega_epsilon")
} else if (x@types$residual == "prec"){
matrices <- c(matrices,"kappa_epsilon")
}
} else if (x@model == "lnm"){
matrices <- "omega_eta"
} else if (x@model == "rnm"){
matrices <- "omega_epsilon"
} else if (x@model == "gvar"){
matrices <- c("beta","omega_zeta")
} else if (x@model == "var1"){
matrices <- c("beta")
if (x@types$zeta == "prec"){
matrices <- c(matrices,"kappa_zeta")
} else if (x@types$zeta == "ggm"){
matrices <- c(matrices,"omega_zeta")
}
} else if (x@model == "panelvar1"){
matrices <- c("beta")
if (x@types$contemporaneous == "prec"){
matrices <- c(matrices,"kappa_zeta")
} else if (x@types$contemporaneous == "ggm"){
matrices <- c(matrices,"omega_zeta")
}
if (x@types$between == "prec"){
matrices <- c(matrices,"kappa_mu")
} else if (x@types$between == "ggm"){
matrices <- c(matrices,"omega_mu")
}
} else if (x@model %in% c("ml_lvm","dlvm1")){
if (x@model == "dlvm1") {
matrices <- c("beta")
} else {
matrices <- character(0)
}
if (x@types$within_latent == "prec"){
matrices <- c(matrices,"kappa_zeta_within")
} else if (x@types$within_latent == "ggm"){
matrices <- c(matrices,"omega_zeta_within")
}
if (x@types$within_residual == "prec"){
matrices <- c(matrices,"kappa_epsilon_within")
} else if (x@types$within_residual == "ggm"){
matrices <- c(matrices,"omega_epsilon_within")
}
if (x@types$between_latent == "prec"){
matrices <- c(matrices,"kappa_zeta_between")
} else if (x@types$between_latent == "ggm"){
matrices <- c(matrices,"omega_zeta_between")
}
if (x@types$between_residual == "prec"){
matrices <- c(matrices,"kappa_epsilon_between")
} else if (x@types$between_residual == "ggm"){
matrices <- c(matrices,"omega_epsilon_between")
}
} else if (x@model == "tsdlvm1"){
matrices <- c("beta")
if (x@types$zeta == "prec"){
matrices <- c(matrices,"kappa_zeta")
} else if (x@types$zeta == "ggm"){
matrices <- c(matrices,"omega_zeta")
}
if (x@types$epsilon == "prec"){
matrices <- c(matrices,"kappa_epsilon")
} else if (x@types$epsilon == "ggm"){
matrices <- c(matrices,"omega_epsilon")
}
} else if (x@model == "Ising"){
matrices <- c("omega")
} else stop("No default argument for 'matrices' for current model.")
}
# Prune first:
if (verbose) message("Pruning model...")
mod_prune <- prune(x,alpha=alpha,verbose=FALSE,runmodel=TRUE,...)
# Combine models:
if (verbose) message("Combining models...")
mod_union <- runmodel(groupequal(combinefun(mod_prune),matrices, verbose = FALSE), verbose = FALSE)
if (verbose) message("Partial pruning...")
curMod <- mod_union
repeat{
pars <- curMod@parameters
# Make a data frame in which the equality free parameters are summed:
miDF <- pars %>% filter(!fixed) %>% group_by(.data[["row"]],.data[["col"]],.data[["matrix"]]) %>%
summarize(mi_free = sum(mi_free)) %>%
arrange(-mi_free)
# Free the best parameter:
propMod <- curMod %>%
groupfree(miDF$matrix[1],miDF$row[1],miDF$col[1]) %>%
runmodel
# Test BIC:
if (propMod@fitmeasures$bic < curMod@fitmeasures$bic){
curMod <- propMod
} else {
break
}
}
mod_partialpooled <- curMod %>% prune(alpha=alpha,verbose=FALSE,runmodel=TRUE,...)
# Select best model:
mods <- list(x, mod_prune, mod_union, mod_partialpooled)
best <- which.min(c(
x@fitmeasures$bic,
mod_prune@fitmeasures$bic,
mod_union@fitmeasures$bic,
mod_partialpooled@fitmeasures$bic
))
bestmod <- mods[[best]]
return(bestmod)
}
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