diff --git a/PhyloSim/src/Makevars.win b/PhyloSim/src/Makevars similarity index 100% rename from PhyloSim/src/Makevars.win rename to PhyloSim/src/Makevars diff --git a/Readme.Rmd b/Readme.Rmd index 8c84b23..153fdf3 100644 --- a/Readme.Rmd +++ b/Readme.Rmd @@ -5,6 +5,8 @@ date: "2024-07-19" output: html_document: keep_md: yes +editor_options: + chunk_output_type: console --- ```{r setup, include=FALSE} @@ -19,24 +21,21 @@ A model, provided as an R package, for the simulation of spatially explicit biog You can install directly from gh, using the 'devtools' package: ```{r, eval = F} -devtools::install_github(repo = "TheoreticalEcology/EcoPhyloSim/", - subdir = "phylosim", +devtools::install_github(repo = "TheoreticalEcology/EcoPhyloSim@v0.3", + subdir = "PhyloSim", dependencies = T, build_vignettes = T) - ?PhyloSim browseVignettes("PhyloSim") ``` -### - +### Example ```{r} library(PhyloSim) # Define a parameter set -par <- createCompletePar(x = 50, y = 50, dispersal = 1 , runs = 1000, - density = 0) +par <- createCompletePar(x = 50, y = 50, dispersal = 1 , runs = 1000) # Run the model simu <- runSimulation(par) @@ -58,7 +57,5 @@ plot(extantPhylogeny) #Look at the species area relation sac(simu, area = c(1,10,100,1000), rep = 100, plot= TRUE) - - ```