In biomodhub/biomod2: Ensemble Platform for Species Distribution Modeling

knitr::opts_chunk$set(echo = TRUE, comment = NA)
options(width = 120)
library(biomod2)
library(kableExtra)

hasBmFiles = !is.na(bm.files)
hasBmMod = !is.na(bm.mod)
hasBmEns = !is.na(bm.ens)
hasBmForm = !is.na(bm.form)
ind.mod = ind.ens = ind.proj = NA
color1 = params.color$color1
color2 = params.color$color2
color3 = params.color$color3

# ind.mod = which(bm.files$file == sub("[.]/", "", bm.mod@link))
ind.mod = which(bm.files$file == sub(paste0(".*", sp.name, "/"), paste0(sp.name, "/"), bm.mod@link))
ind.proj = which(bm.files$type == "projection" &
                   bm.files$refer_to == bm.files$refer_to[ind.mod])
name.proj = unique(bm.files$ID[ind.proj])

ind.ens = which(bm.files$type == "models" &
                        bm.files$level == "ensemble" &
                        bm.files$refer_to == bm.files$refer_to[ind.mod])

fun_call <- function(myCall, myName, ntab = 4) {
  mess = deparse(myCall)
  mess = paste0(mess, collapse = "")
  mess = gsub("    ", "", mess)
  mess = gsub(", ", "\n, ", mess)
  mess = gsub("\n, \"", ", \"", mess)

  mess = paste0(myName, " <- ", mess)
  mess = gsub("\n,", paste0("\n", paste0(rep("\t", ntab), collapse = "")), mess)
  return(mess)
}

tab = knitr::kable(bm.files[, c("file", "path", "type", "level", "ID")], format = "html")
tab = kable_styling(tab, bootstrap_options = "condensed")
if (any(!is.na(c(ind.mod, ind.ens)))) {
  row_spec(tab, c(ind.mod, ind.ens), bold = TRUE, color = color1)
}

Formated data

cat(fun_call(bm.form@call, "myBiomodData", 10))

Single models

cat(fun_call(bm.mod@call, "myBiomodModelOut", 10))

Ensemble models

cat(fun_call(bm.ens@call, "myBiomodEM", 10))

Projections

tab = knitr::kable(bm.files[, c("file", "path", "type", "level", "ID")], format = "html")
tab = kable_styling(tab, bootstrap_options = "condensed")
if (any(!is.na(ind.proj))) {
  row_spec(tab, ind.proj, bold = TRUE, color = color3)
}

for (proj.i in name.proj) {
  ind.proj.i = intersect(ind.proj, which(bm.files$ID == proj.i))
  for (j in ind.proj.i) {
    bm.proj = get(load(file = bm.files$file[j]))
    if (inherits(try(bm.proj@data.type), "try-error")) {
      bm.proj@data.type <- "binary"
    }
    cat(fun_call(bm.proj@call, "myBiomodProj", 10))
    cat("\n\n")
  }
}
rm(list = basename(bm.files$file))