R/DAISIE_ONEcolonist_nonoceanic.R

In joshwlambert/DAISIEsim:

DAISIE_ONEcolonist_nonoceanic = function(time,island_spec,stt_table, keep_final_state = FALSE, nonend_spec, end_spec)
{

  ### number of independent colonisations
  uniquecolonisation = as.numeric(unique(island_spec[,"Colonisation time (BP)"]))
  number_colonisations = length(uniquecolonisation)

  ### if there is only one independent colonisation - anagenetic and cladogenetic
  #species are classed as stac=2; immigrant classed as stac=4:
  if(number_colonisations == 1)
  {
    if (island_spec[1,"Species type"] == "I")
    {
      descendants = list(stt_table = stt_table,
                         branching_times = c(time,as.numeric(island_spec[1,"Colonisation time (BP)"])),
                         stac = 4,
                         missing_species = 0,
                         nonend_spec = nonend_spec,
                         end_spec = end_spec)
    }
    if (island_spec[1,"Species type"] == "A")
    {
      descendants = list(stt_table = stt_table,
                         branching_times = c(time,as.numeric(island_spec[1,"Colonisation time (BP)"])),
                         stac = 2,
                         missing_species = 0,
                         nonend_spec = nonend_spec,
                         end_spec = end_spec)
    }
    if (island_spec[1,"Species type"] == "C")
    {
      descendants = list(stt_table = stt_table,
                         branching_times = c(time,rev(sort(as.numeric(island_spec[,"branching time (BP)"])))),
                         stac = 2,
                         missing_species = 0,
                         nonend_spec = nonend_spec,
                         end_spec = end_spec)
    }
  }

  ### if there are two or more independent colonisations, all species are classed as stac=3 and put within same list item:
  if(number_colonisations > 1)
  {
    descendants = list(stt_table = stt_table,
                       branching_times = NA,
                       stac = 3,
                       missing_species = 0,
                       other_clades_same_ancestor = list(),
                       nonend_spec = nonend_spec,
                       end_spec = end_spec)

    btimes_all_clado_desc = rev(sort(as.numeric(island_spec[,'branching time (BP)'])))

    if(length(btimes_all_clado_desc)!=0) { descendants$branching_times= c(time, btimes_all_clado_desc)}
    if(length(btimes_all_clado_desc)==0) { descendants$branching_times= c(time, max(as.numeric(island_spec[,"Colonisation time (BP)"])))}

    ### create table with information on other clades with same ancestor, but this information is not used in DAISIE_ML
    oldest = which(as.numeric(island_spec[,"Colonisation time (BP)"]) == max(as.numeric(island_spec[,"Colonisation time (BP)"])))

    youngest_table = island_spec[-oldest,]
    if(class(youngest_table)=='character')
    {
      youngest_table = t(as.matrix(youngest_table))
    }

    uniquecol = as.numeric(unique(youngest_table[,"Colonisation time (BP)"]))

    for(colonisation in 1:length(uniquecol))
    {
      descendants$other_clades_same_ancestor[[colonisation]] = list(brts_miss = NA,species_type = NA)

      samecolonisation = which(as.numeric(youngest_table[,"Colonisation time (BP)"]) == uniquecol[colonisation])

      if (youngest_table[samecolonisation[1],"Species type"] == "I")
      {
        descendants$other_clades_same_ancestor[[colonisation]]$brts_miss = as.numeric(youngest_table[samecolonisation,"Colonisation time (BP)"])
        descendants$other_clades_same_ancestor[[colonisation]]$species_type = "I"
      }

      if (youngest_table[samecolonisation[1],"Species type"] == "A")
      {
        descendants$other_clades_same_ancestor[[colonisation]]$brts_miss =  as.numeric(youngest_table[samecolonisation,"Colonisation time (BP)"])
        descendants$other_clades_same_ancestor[[colonisation]]$species_type = "A"
      }

      if (youngest_table[samecolonisation[1],"Species type"] == "C")
      {
        descendants$other_clades_same_ancestor[[colonisation]]$brts_miss = rev(sort(as.numeric(youngest_table[samecolonisation,"branching time (BP)"])))
        descendants$other_clades_same_ancestor[[colonisation]]$species_type = "C"
      }
    }
  }
  #### ADDS island_spec ####
  if (keep_final_state == TRUE) {
    descendants$island_spec <- island_spec
  }
  return(descendants)
}