R/multimaxent.formula.R

In YunyiShen/multiMaxEnt: Multispecies MaxEnt Model Via Gibbs Point Process

#' @export
maxent.formula <-
function(p, data, classes="default")
{
   cont <- names(data)[sapply(data,class)!="factor"]
   categorical <- names(data)[sapply(data,class)=="factor"]
   np <- min(summary(p[,3]))/2
   if (classes=="default") {
      if (np < 10) classes <- "l"
      else if (np < 15) classes <- "lq"
      else if (np < 80) classes <- "lqh"
      else classes <- "lqph"
   }
   terms <- NULL
   if (length(cont)) {
      if (grepl("l", classes))
         #terms <- c(terms, paste(paste0("marks:",cont),collapse=" + "))
         terms <- c(terms, paste(paste0("",cont),collapse=" + "))
      if (grepl("q", classes))
         #terms <- c(terms, paste("marks:I(",cont,"^2)",sep="",collapse=" + "))
         terms <- c(terms, paste("I(",cont,"^2)",sep="",collapse=" + "))
      if (grepl("h", classes))
         #terms <- c(terms, paste("marks:hinge(",cont,")",sep="",collapse=" + "))
         terms <- c(terms, paste("hinge(",cont,")",sep="",collapse=" + "))
      if (grepl("t", classes))
         #terms <- c(terms, paste("marks:thresholds(",cont,")",sep="",collapse=" + "))
         terms <- c(terms, paste("thresholds(",cont,")",sep="",collapse=" + "))
      if (grepl("p", classes)) {
         m <- outer(cont, cont, function(x,y) paste(x,y,sep=":"))
         terms <- c(terms, m[lower.tri(m)])
      }
   }
   if (length(categorical))
      #terms <- c(terms, paste("marks:categorical(",categorical,")",sep="",collapse=" + "))
      terms <- c(terms, paste("categorical(",categorical,")",sep="",collapse=" + "))
   #formula(paste("~marks +", paste(terms, collapse = " + "), "-1")) # we want different first order potential for each species (i.e. "marks")
   formula(paste("~", paste(terms, collapse = " + "), "-1")) # we want different first order potential for each species (i.e. "marks")
}