Updated README.md

README.md

@@ -9,20 +9,63 @@ Persephone models farmers' decision making and its impact on species in agricult
 landscapes. The aim is to investigate how policies such as the CAP influence farms and
 biodiversity.
 
-It is currently in the very early stages of development.
+The model is based on the [Agents.jl](https://juliadynamics.github.io/Agents.jl/stable/) 
+framework. It is currently in the very early stages of development.
 
 ## Usage
 
+### Installation
+
 Install the latest version of the [Julia](https://julialang.org/downloads/) programming 
 language. The recommended editors are [VSCode](https://www.julia-vscode.org/) or
 [Emacs](https://www.emacswiki.org/emacs/JuliaProgrammingLanguage) (see `docs/editors.md`).
 To install package dependencies, open a Julia REPL in this folder and run 
 `using Pkg; Pkg.activate("."); Pkg.instantiate()`.
 
-Run the simulation by executing `run.jl` from the commandline, or loading it from
-within a Julia REPL with `include("run.jl")`. 
+### Running from the commandline
+
+This is the normal mode of operation. Simply execute `run.sh`, typically like so (in Linux):
+
+```
+> ./run.sh -c <config>
+```
+
+where `<config>` specifies the configuration file to use. The full list of commandline
+arguments is:
+
+```
+usage: run.jl [-c CONFIGFILE] [-s SEED] [-m MAPFILE] [-o OUTDIR]
+              [-l LOGLEVEL] [-r RUNTIME] [--version] [-h]
+
+optional arguments:
+  -c, --configfile CONFIGFILE
+                        name of the configuration file
+  -s, --seed SEED       inital random seed (type: Int64)
+  -m, --mapfile MAPFILE
+                        name of the map file
+  -o, --outdir OUTDIR   location of the output directory
+  -l, --loglevel LOGLEVEL
+                        verbosity: "debug", "info", or "errors"
+  -r, --runtime RUNTIME
+                        duration in days that the simulation will run
+                        (type: Int64)
+  --version             show version information and exit
+  -h, --help            show this help message and exit
+
+```
+
+### Running from within Julia
+
+To use the model from within Julia (either inside an interactive REPL or if you want
+to import it from your own software), do the following:
+
+```julia
+using Pkg
+Pkg.activate(".") # assuming you're in the Persephone root folder
+using Persephone
+```
 
-This model uses the [Agents.jl](https://juliadynamics.github.io/Agents.jl/stable/) framework.
+You can then access all Persephone functions, such as `simulate()`.
 
 ---