Configs.md

@@ -5,7 +5,7 @@ Configs
 
 # 1.1 Initialisation
 
-### 1.1.1 Pantropical diversity (Hagen and Skeels et al 2021)
+### 1.1.1  Global equatorial ancestor (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
@@ -36,7 +36,7 @@ create_ancestor_species <- function(landscape, config) {
 
 # 1.2 Dispersal
 
-### 1.2.1 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 +50,7 @@ get_dispersal_values <- function(n, species, landscape, config) {
 
 # 1.3 Evolution
 
-### 1.3.1 Pantropical diversity (Hagen and Skeels et al 2021)
+### 1.3.1 Pantropical diversity (Brownian Motion (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
@@ -75,7 +75,7 @@ apply_evolution <- function(species, cluster_indices, landscape, config) {
 
 # 1.4 Speciation
 
-### 1.4.1 Pantropical diversity (Hagen and Skeels et al 2021)
+### 1.4.1 Linear divergence (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.
 
@@ -92,7 +92,7 @@ get_divergence_factor <- function(species, cluster_indices, landscape, config) {
 
 # 1.5 Ecology
 
-### 1.5.1 Pantropical diversity (Hagen and Skeels et al 2021)
+### 1.5.1 Temperature and aridity thresholds (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.