Configs.md

@@ -6,6 +6,8 @@ Configs
 # 0. Complete configs
  ### 0.1 Pantropical Diversity, Hagen and Skeels et al 2021 
 
+[https://doi.org/10.1073/pnas.2026347118](https://www.pnas.org/content/118/40/e2026347118.short)
+
 [config template](https://gitlab.ethz.ch/ites-le/gen3sis/gen3sis_wiki/-/blob/master/configs/Pantropical_config_template.R)
  
 [config generator](https://gitlab.ethz.ch/ites-le/gen3sis/gen3sis_wiki/-/blob/master/configs/ESH_config_generator.R)
@@ -23,7 +25,7 @@ config templates: [M0](https://gitlab.ethz.ch/ites-le/gen3sis/gen3sis_wiki/-/blo
 
 This function intialises a single species that occupies all non-arid equatorial grid cells.
 
-Required traits: dispersal, temp, temp_width
+Required traits: *dispersal*, *temp*, *temp_width*
 
 ~~~R
 
@@ -51,7 +53,7 @@ create_ancestor_species <- function(landscape, config) {
 
 This function intialises a single species that occupies all global grid cells.
 
-Required traits: dispersal, temp, prec, body_size
+Required traits: *dispersal*, *temp*, *prec*, *body_size*
 
 ~~~R
 
@@ -131,15 +133,15 @@ apply_evolution <- function(species, cluster_indices, landscape, config) {
 
 ### 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).
+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).
 
 Explored paramters:  
 params$sigma_squared_bs = [0.001, 0.02]
 params$sigma_squared_t = [0.001, 0.015]
 params$psi = 0
 
-Required traits: temp and body_size
-Requires environment: temperature (temp) 
+Required traits: *temp* and *body_size*
+Requires environment: *temp*
 
 ~~~R
 sigma_squared_bs <-  params$sigma_squared_bs
@@ -199,8 +201,8 @@ Explored paramters:
 params$divergence_threshold = [2,10] 
 params$lambda = [2,5]
 
-Required traits: body_size
-Required environment: temperature (temp) 
+Required traits: *body_size*
+Required environment: *temp*
 
 ~~~R
 divergence_threshold =  params$divergence_threshold
@@ -239,7 +241,7 @@ Explored paramters:
 params$divergence_threshold = [2,10] 
 params$lambda = [2,5]
 
-Required traits: body_size
+Required traits: *body_size*
 Required environment: temperature (temp) 
 ~~~R
 divergence_threshold =  params$divergence_threshold
@@ -282,7 +284,7 @@ Explored paramters:
 params$divergence_threshold = [2,10] 
 params$lambda = [2,5]
 
-Required traits: body_size and temperature
+Required traits: *body_size* and *temperature*
 Required environment: temperature (temp) 
 
 ~~~R
@@ -363,7 +365,7 @@ params$aridity_cost = 2
 params$inflexion = 1000
 params$decay = 0.1
 
-Rrequired traits: temp, body_size
+Rrequired traits: *temp*, *body_size*
 Required Environments: tmeperature (temp), aridity (prec)
 ~~~R