added function clean_world, and beta and alpha diversity ( to be continued)....

added function clean_world, and beta and alpha diversity ( to be continued). Modified Plots.plot, mainly for integrating the geotrait into option "x" and "xs"

src/ABMEv.jl

@@ -18,7 +18,7 @@ module ABMEv
     export MixedAgent,StdAgent,Agent,get_fitness,get_x,get_dim,get_nancestors,get_xarray,get_xhist,
         get_geo,get_b,get_d,increment_x!,get_inc_reflected,world2df,
         split_move,split_merge_move,tin,new_world_G
-    export copy,runWorld_store_WF,runWorld_store_G #,runWorld_G!,runWorld_WF!,
+    export copy,runWorld_store_WF,runWorld_store_G,clean_world #,runWorld_G!,runWorld_WF!,
     export H_discrete,findclusters,var,covgeo,hamming
     export update_afterbirth_std!,update_afterdeath_std!
     export generalised_gaussian,gaussian,ma,eth_grad_std

src/ABMEv_Agent.jl

@@ -36,11 +36,11 @@ function new_world_G(nagents::Int,p::Dict; spread = 1., offset = 0.)
 end
 
 # returns trait i of the agent
-get_x(a::Agent,i::Number) = a.x_history[Int(i),end]
-get_x(a::Agent) = a.x_history[:,end]
 get_xhist(a::Agent,i::Number) = a.x_history[Int(i),:]
 get_xhist(a::Agent) = a.x_history
+get_x(a::Agent) = a.x_history[:,end]
 get_geo(a::Agent) = sum(get_xhist(a,1))
+get_x(a::Agent,i::Number) = i > 0 ? a.x_history[Int(i),end] : get_geo(a)
 get_d(a::Agent) = a.d
 get_b(a::Agent) = a.b
 get_fitness(a::Agent) = a.b - a.d
@@ -48,12 +48,13 @@ get_dim(a::Agent) = size(a.x_history,1)
 get_nancestors(a::Agent) = size(a.x_history,2)
 """
     get_xarray(world::Array{Agent},trait::Int)
+If trait = 0 , we return the geotrait.
 Mainly works for WF-type world
 Returns trait of every agents of world in the form of an array which dimensions corresponds to the input.
 Particularly suited for an array world corresponding to a timeseries.
 
 """
-get_xarray(world::Array{T},trait::Int) where {T <: Agent}= reshape(hcat(get_x.(world,trait)),size(world,1),size(world,2))
+get_xarray(world::Array{T},trait::Int) where {T <: Agent} = trait > 0 ? reshape(hcat(get_x.(world,trait)),size(world,1),size(world,2)) : reshape(hcat(get_geo.(world)),size(world,1),size(world,2))
 
 """
     get_xarray(world::Array{Agent,1})

src/ABMEv_Gillepsie.jl

@@ -70,3 +70,10 @@ function updateWorld_G!(world,p,update_rates!,t)
         return -1.
     end
 end
+
+"""
+    clean_world(world::Array{T}) where {T <: Agent}
+Get rid of missing value in `world`
+"""
+#TODO : put some type specs here
+clean_world(world) = collect(skipmissing(world))

src/ABMEv_metrics.jl

@@ -42,6 +42,7 @@ function findclusters(v::Vector,allextrema =true)
 end
 
 import Statistics.var
+# TODO: rename this to gamma diversity
 """
     var(world::Array{Agent};trait=:)
 If trait = 0, returns the variance of the geotrait,
@@ -89,3 +90,24 @@ function hamming(world::Array{Agent,1}) where T <: Int
     end
     return H
 end
+"""
+    get_alpha_div(world::Array{U,1};trait=1) where U <: Union{Missing,Agent{T}} where T
+# Arguments
+"""
+function get_alpha_div(world::Array{U,1};trait=1) where U <: Union{Missing,Agent{T}} where T
+    _xall_df = world2df(world,geotrait=true)
+    xall_per_patch = groupby(_xall_df, :x1,sort=true)
+    #TODO: to be continued
+end
+
+"""
+    get_beta_div(world::Array{U,1};trait=1) where U <: Union{Missing,Agent{T}} where T
+# Arguments
+"""
+function get_beta_div(world::Array{U,1};trait=1) where U <: Union{Missing,Agent{T}} where T
+    _xall_df = world2df(world,geotrait=true)
+    xall_per_patch = groupby(_xall_df, :x1,sort=true)
+    sbar_i = [mean(xp.x2) for xp in xall_per_patch]
+
+    #TODO: to be continued
+end

src/ABMEv_plot.jl

@@ -6,9 +6,13 @@ import KernelDensity:kde,pdf
 
 # ARGS
 - `what = ["x","H"]`: the plots you want to obtain
-- `trait = 1`: the trait that will plotted regarding what you asked
+- `trait = 1`: the trait that will plotted regarding what you asked. `trait = 0` will plot the geotrait
 - `tplot = false` used when calling xs, as it plots a snapshot of the world at a particular time
 It should correspond to an integer, as it indexes the column to plot
+
+# Options available
+- `"x"`
+- `"xs"`
 """
 
 @recipe function plot(world::Array{U},p;what=["x","H"],trait = 1,tplot = 0) where U <: Union{Missing,Agent}
@@ -52,9 +56,15 @@ It should correspond to an integer, as it indexes the column to plot
     # world should be a one dimensional vector, corresponding to one time step only
     if "xs" in what
         d_i = []; xt_array = []; x1_array = []
-        world_df_g = groupby(world2df(collect(skipmissing(world[:, tplot > 0 ? tplot : size(world,2) ]))),:x1)
+        world_df_g = groupby(world2df(collect(skipmissing(world[:, tplot > 0 ? tplot : size(world,2) ])),geotrait=true),:x1)
         for world_df in world_df_g
-            x = world_df.x2 ; x1 =  world_df.x1
+            if trait == 0
+                x = world_df.g
+            else
+                # fitness occupies first spot
+                x = world_df[:,trait+1] ;
+            end
+            x1 =  world_df.x1;
             append!(d_i,pdf(kde(x),x))
             append!(xt_array,x)
             append!(x1_array,x1)
@@ -74,20 +84,6 @@ It should correspond to an integer, as it indexes the column to plot
             x1_array[:],xt_array[:]
         end
     end
-    if "geo" in what
-        @series begin
-        xarray = get_geo.(world_sm)
-            seriestype := :scatter
-            markercolor := "blue"
-            markerstrokewidth := 0
-            seriesalpha :=.1
-            xlabel := "time"
-            ylabel := "trait value"
-            label := ""
-            # markersize := 2.3/1000*size(world_sm,1)
-            tspan_ar[:],xarray[:]
-        end
-    end
     if "3dgeo" in what
         @series begin
         xarray = get_geo.(world_sm)