Configs.md

@@ -34,9 +34,44 @@ create_ancestor_species <- function(landscape, config) {
 }
 ~~~
 
+### 1.1.2
+
+Global ancestor (Evolutionary Speed Hypothesis, Skeels et al 2021)
+
+This function intialises a single species that occupies all global grid cells.
+Requires 4 traits: dispersal, temp, prec, body_size
+
+~~~R
+
+create_ancestor_species <- function(landscape, config) {
+  #browser()
+  # set up a raster of global temperatures 
+  t_world <- raster::rasterFromXYZ(cbind(landscape$coordinates,landscape$environment[, 1, drop = F]))
+  t_world <- extend(t_world, landscape$extent)
+  
+  # Will the simulation sample the ancestor from a partcular continent or randomly from anywhere?
+  start_cells <- as.character(Which(t_world, cells=T))
+  
+  # now fill the list of new species
+  all_species <- list()
+  
+  new_species <- create_species(as.character(start_cells), config)
+  new_species$traits[ , "dispersal"] <- 1
+  new_species$traits[ , "temp"] <- landscape$environment[start_cells, "temp"]
+  new_species$traits[ , "prec"] <- landscape$environment[start_cells, "prec"]
+  new_species$traits[ , "body_size"] <- 0.2
+  
+  all_species <- append(all_species, list(new_species))
+  
+  
+  return(all_species)
+  
+}
+~~~
+
 # 1.2 Dispersal
 
-### 1.2.1 (Weibull dispersal kernel (Pantropical diversity, Hagen and Skeels et al 2021)
+### 1.2.1 Weibull dispersal kernel (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
@@ -50,7 +85,7 @@ get_dispersal_values <- function(n, species, landscape, config) {
 
 # 1.3 Evolution
 
-### 1.3.1 Pantropical diversity (Brownian Motion (Hagen and Skeels et al 2021)
+### 1.3.1 Species-level Brownian Motion (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
@@ -70,9 +105,47 @@ apply_evolution <- function(species, cluster_indices, landscape, config) {
   return(traits)
   
 }
-
 ~~~
 
+### 1.3.2 Cluster-level OU + BM (Evolutionary Speed Hypothesis, Skeels et al 2021)
+
+This function evolves a temperature-niche trait under a Ornstein Uhlenbeck model of trait evolution and evolves a body size trait under a Brownian Motion model. The OU model has a random walk element as in the Brownian motion model and also a parameter (psi) that draws the value towards an optimal value (based on the mean temperature value across the clusters geographic range). When psi=0 OU = BM. The OU and BM models each have an independant rate parameter (sigma squared). This function evolves each geographic cluster seperately (instead of each species speerately or each grid cell seperately).
+
+Requires 2 traits: temp and body_size
+Specify paramters:  params$sigma_squared_bs, params$sigma_squared_t, params$psi
+
+
+sigma_squared_bs <-  params$sigma_squared_bs
+sigma_squared_t <-  params$sigma_squared_t
+psi <-  params$psi
+
+apply_evolution <- function(species, cluster_indices, landscape, config) {
+  
+  # cell names
+  traits <- species[["traits"]]
+  cells <- rownames( traits )
+  
+  # evolve traits for each cluster
+  for(cluster_index in unique(cluster_indices)){
+    cells_cluster <- cells[which(cluster_indices == cluster_index)]
+    t_theta_cluster <- mean(landscape$environment[cells_cluster,"temp"], na.rm=T)
+    # evolve temperature
+    traits[cells_cluster, "temp"] <- traits[cells_cluster, "temp"] + ( psi * (t_theta_cluster - traits[cells_cluster, "temp"]) ) + rnorm(1, mean = 0, sd = sigma_squared_t)
+    # evolve body size
+    traits[cells_cluster, "body_size"] <- traits[cells_cluster, "body_size"] + rnorm(1, mean = 0, sd = sigma_squared_bs)
+  }
+  
+  # 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}
+  if(any(traits[, "body_size"] > 1)){traits[which(traits[,"body_size"]>1), "body_size"] <- 1}
+  if(any(traits[, "body_size"] < 0)){traits[which(traits[,"body_size"]< 0), "body_size"] <- 0}
+  
+  return(traits)
+  
+}
+
+
 # 1.4 Speciation
 
 ### 1.4.1 Linear divergence (Pantropical diversity, Hagen and Skeels et al 2021)