1. Set-up | Landscape | Configuration | 2. Run | 3. Visualize | 4. Analyze

1. Create an empty config | Content of config_empty.R | Version: 1.0 | Author: | Date: | Landscape: | Publications: | Description: | set the random seed for the simulation. | set the starting time step or leave NA to use the earliest/highest time-step. | set the end time step or leave as NA to use the latest/lowest time-step (0). | maximum total number of species in the simulation before it is aborted. | maximum number of species within one cell before the simulation is aborted. | a list of traits to include with each species. | a "dispersal" trait is implicitly added in any case. | ranges to scale the input environments with: | not listed variable: no scaling takes place | listed, set to NA: env. variable will be scaled from [min, max] to [0, 1] | listed with a given range r: env. variable will be scaled from [r1, r2] to [0, 1] | the list of all species can be found in data$all_species. | the current landscape can be found in data$landscape. | the initial abundance of a newly colonized cell, both during setup and later when | colonizing a cell during the dispersal. | place species in the landscape: | Dispersal | the maximum range to consider when calculating the distances from local distance inputs. | returns n dispersal values. | Speciation | threshold for genetic distance after which a speciation event takes place. | factor by which the divergence is increased between geographically isolated population. | can also be a matrix between the different population clusters. | Evolution | mutate the traits of a species and return the new traits matrix. | Ecology | called for every cell with all occurring species, this function calculates abundances and/or who survives for each sites | returns a vector of abundances. | set the abundance to 0 for every species supposed to die. | 2. Explain example config | Content of config_.empty_southamerica.R | Metadata | Author: Oskar Hagen | Date: 26.10.2020 | Landscape: SouthAmerica | Publications: R-package gen3sis | Description: Example config used at the introduction vignette and similar to case study global configs in Hagen et al. 2020. | O. Hagen, B. Flück, F. Fopp, J.S. Cabral, F. Hartig, M. Pontarp, T.F. Rangel, L. Pellissier. gen3sis: the general engine for eco-evolutionary simulations on the origins of biodiversity. | Settings | Observer | Initialization | Core Processes | mutate the traits of a species and return the new traits matrix | 3. Modify a config

Creating the environmental rasters bricks | Creating a list with the environmental raster bricks | Defining a cost function | Further useful arguments | Create input files

Create your landscape grid | Add environmental characteristics | Add a cost function