Configs.md

-Configs
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+Configs
+
+
+[[_TOC_]]
+
+# 1.1 Initialisation
+
+### 1.1.1 Pantropical diversity (Hagen and Skeels et al 2021)
+
+This function intialises a single species that occupies all non-arid equatorial grid cells.
+Requires 3 traits: dispersal, temp, temp_width
+Specify paramters:  params$initialAbundance
+
+~~~R
+initial_abundance = params$initialAbundance
+
+create_ancestor_species <- function(landscape, config) {
+
+ p_world <- raster::rasterFromXYZ(cbind(landscape$coordinates[which(landscape$coordinates[,2] > -23.5 & landscape$coordinates[,2] < 23.5),], 
+                                         landscape$environment[which(landscape$coordinates[,2] > -23.5 & landscape$coordinates[,2] < 23.5), 1, drop = F]))
+  p_world <- extend(p_world, landscape$extent)
+  mesic_equatorial_cells <- as.character(Which(p_world, cells=T))
+
+  all_species <- list()
+
+  new_species <- create_species(NA, as.character(mesic_equatorial_cells), config)
+  new_species$traits[ , "dispersal"] <- 1
+  new_species$traits[ , "temp"] <- landscape$environment[mesic_equatorial_cells, "temp"]
+  new_species$traits[ , "prec"] <- 0
+  new_species$traits[ , "temp_width"] <- params$TW
+  all_species <- append(all_species, list(new_species))
+
+  return(all_species)
+}
+~~~
+
+# 1.2 Dispersal
+
+### 1.2.1 Pantropical diversity (Hagen and Skeels et al 2021)
+
+This function draws the dispersal kernel from a Weibull distriution with shape and scale parameters.
+Specify paramters: params$WeibullShape, params$WeibullScale
+~~~R
+
+get_dispersal_values <- function(n, species, landscape, config) {
+  values <- rweibull(n, shape = params$WeibullShape, scale = params$WeibullScale)
+  return(values)
+}
+~~~
+
+# 1.3 Evolution
+
+### 1.3.1 Pantropical diversity (Hagen and Skeels et al 2021)
+
+This function evolves a single temperature-niche trait under a random walk (Brownian Motion) model.
+Requires 1 trait: temp
+Specify paramters:   params$Tev
+
+~~~R
+apply_evolution <- function(species, cluster_indices, landscape, config) {
+  
+  traits <- species[["traits"]]
+  traits[, "temp"] <- traits[, "temp"] + rnorm(1, mean = 0, sd = params$Tev)
+  
+  # set bounds between 0 and 1 so the species can;t evolve a niche beyond that present in the data (all temp is scaled between 0 and 1)
+  if(any(traits[, "temp"] > 1)){traits[which(traits[,"temp"]>1), "temp"] <- 1}
+  if(any(traits[, "temp"] < 0)){traits[which(traits[,"temp"]<0), "temp"] <- 0}
+ 
+  
+  return(traits)
+  
+}
+
+~~~
+
+# 1.4 Speciation
+
+### 1.4.1 Pantropical diversity (Hagen and Skeels et al 2021)
+
+This function increases divergence between populations by 0.1 at each timestep and speciation occurs after divergence crosses threshold S. Values < 1 mean populations seperate more slowly than they come back toegther, as populations that come into secondary contact seperate at rate of 1 per time step.
+
+Specify paramters:   params$S
+Requires 2 traits: temp, temp_width
+
+~~~R
+divergence_threshold = params$S
+
+get_divergence_factor <- function(species, cluster_indices, landscape, config) {
+  return(0.1)
+}
+~~~
+
+# 1.5 Ecology
+
+### 1.5.1 Pantropical diversity (Hagen and Skeels et al 2021)
+
+This function determines whether species can occupy a grid cell based on the temperature niche trait and width as well as aridity. Species can occupy cells of the temp niche + or - the temp width. A further constraint is added where species cannot occupy arid grid cells. 
+
+Requires environment: temperature (temp) and aridity (prec)
+
+~~~R
+apply_ecology <- function(abundance, traits, landscape, config) {
+  temp_diff <- abs( traits[, "temp"] - landscape[, "temp"])
+  abundance <- temp_diff < traits[, "temp_width"] 
+  abundance[which(landscape[, "prec"] > 0.5)] <- 0
+  return(abundance)
+}
+~~~
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