Merge pull request #9 from geeklhem/popdyn

Added a simple population dynamics model.

README

@@ -5,10 +5,10 @@ to organize iterated prisoner's dilemma competition between different
 strategies.
 
 It has been written for the "[Mathematics and Biology Workgroup](http://www.gt-mathsbio.biologie.ens.fr/)" in the
-École normale supérieure (Paris, France) and it gives [this kind of output](http://www.eleves.ens.fr/home/doulcier/projects/math/ipdt.html).
+École normale supérieure (Paris, France) and it gives [this kind](http://www.eleves.ens.fr/home/doulcier/projects/math/ipdt.html) [of output](http://www.eleves.ens.fr/home/doulcier/projects/math/popdyn.html ).
 
 ## How to 
-### Just test it
+### Play around
 To test it, if you have python2.7 and pip available the installation is quite simple:
 
 ```bash
@@ -36,7 +36,21 @@ $ ipdt tournament --exclude naivecoop defector
 
 ``` 
 
-You can also run a single match between two strategies:
+We have implemented a small model of population dynamics:
+
+- The payoffs are computed by a simple tournament.
+- Each strategies start with an equal proportion in the population.
+- Each generation, the geometric growth of their relative abundance is given
+  by their payoffs weighted by the encounter probability (product of abundances).
+
+```bash
+# Run a population dynamics model for 10 generations with a null mutation level.
+$ ipdt popdyn --generations 10 --mu 0
+```
+
+
+Finally, you can also run a single match between two strategies:
+
 ```bash
 $ ipdt match -p naivecoop randomplayer
 ```
@@ -46,7 +60,7 @@ If you want more detailed info on the output, you can use the options
 `-vv` info or `-vvv` debug.
 
 You can have a [nice HTML5
-export](http://www.eleves.ens.fr/home/doulcier/projects/math/ipdt.html) by
+export](http://www.eleves.ens.fr/home/doulcier/projects/math/ipdt.html) (and [for population dynamics](http://www.eleves.ens.fr/home/doulcier/projects/math/popdyn.html)) by
 using the `--html filename` option: it will create a `filename.html`
 file in your current folder.
 

bin/ipdt

@@ -19,7 +19,7 @@ parser = argparse.ArgumentParser(description=__doc__,formatter_class=argparse.Ra
 parser.add_argument('command',
                     help='Command',
                     type=str,
-                    choices=['tournament', 'list', 'match'])
+                    choices=['tournament', 'list', 'match', 'popdyn'])
 parser.add_argument('-p','--players',
                     nargs="*",
                     default=[],
@@ -28,7 +28,6 @@ parser.add_argument('-e','--exclude',
                     nargs="*",
                     default=[],
                     help="Strategies to exclude codenames")
-
 parser.add_argument('-v','--verbose',
                     help='Verbosity level : -v warning, -vv info, -vvv debug',
                     action="count",
@@ -37,6 +36,15 @@ parser.add_argument('-T','--turns',
                     type=int,
                     help='Number of turns',
                     default=100)
+parser.add_argument('--mu',
+                    type=float,
+                    help='Mutation level (used only if command is popdyn).',
+                    default=0)
+
+parser.add_argument('-g','--generations',
+                    type=int,
+                    help='Number of generations (used only if command is popdyn).',
+                    default=100)
 parser.add_argument('--replicas',
                     type=int,
                     help='Number of repetition of the tournament',
@@ -76,11 +84,14 @@ logger.addHandler(ch)
 import ipdt.tournament
 import ipdt.players
 import ipdt.export
+import ipdt.popdyn
 
 # === SET THE PARAMETERS ===
 param = {}
 param["T"] = args.turns
 param["replicas"] = args.replicas
+param["generations"] = args.generations
+param["mu"] = args.mu
 
 # Payoff matrix 
 order = ["cc","cd","dc","dd"]
@@ -94,45 +105,51 @@ if len(args.players) == 0:
 if len(args.exclude) != 0:
     args.players = list(set(args.players) - set(args.exclude))
 
+players = [ getattr(ipdt.players, name).Player for name in args.players]
+if args.html:
+    info = {}
+    for code,P in zip(args.players,players):
+        info[P.name] = {"author":P.author,
+                        "name":P.name,
+                        "code":code,
+                        "description":P.__doc__}
+
 
 if args.command == "match":   
-    if hasattr(ipdt.players, args.players[0]):
-       P1= getattr(ipdt.players, args.players[0]).Player
-    if hasattr(ipdt.players, args.players[1]):
-       P2= getattr(ipdt.players, args.players[1]).Player
-
-    payoff = ipdt.tournament.match(P1,P2,param)
+    payoff = ipdt.tournament.match(players[0],players[1],param)
     if payoff[0]>payoff[1]:
-        winner = "P1"
+        winner = players[0].name
     elif payoff[0]==payoff[1]:
         winner = "NOBODY"
     else:
-        winner = "P2" 
-    print("Match endend: {} WINS !".format(winner))
+        winner = players[1].name
+    print("{} vs {}: {} WINS !".format(players[0].name,players[1].name,winner))
     logger.info("Payoffs: {}".format(payoff))
 
 if args.command == "tournament":
-    players = [ getattr(ipdt.players, name).Player for name in args.players]
     ranking,details = ipdt.tournament.tournament(players,param)
     print("Tournament ended ! Ranking:")
     for n,(score,name) in enumerate(ranking):
         print("{}: {} ({} points)".format(n+1,name,score))
 
     if args.html:
-        info = {}
-        for code,P in zip(args.players,players):
-            info[P.name] = {"author":P.author,
-                            "name":P.name,
-                            "code":code,
-                            "description":P.__doc__}
         exporter = ipdt.export.HTMLexporter(args.html+".html",
                                             ranking,
                                             details,
                                             param,
                                             info)
         exporter.save()
 
-
+if args.command == "popdyn":
+    time_series, details = ipdt.popdyn.popdyn(players,param)
+
+    if args.html:
+        exporter = ipdt.export.HTMLexporterTS(args.html+".html",
+                                              time_series,
+                                              details,
+                                              param,
+                                              info)
+        exporter.save()    
 
 if args.command == "list":
     print("Available strategies are:")

ipdt/export.py

@@ -125,6 +125,27 @@
   font-family:monospace;
   text-align:left;
 }
+
+#chart svg {
+  height: 600px;
+}
+
+table{
+margin: auto;
+}
+
+#ts th, #ts td {
+  color: black;
+  text-align:center;
+  background-color: white;
+}
+
+.'twhite'{
+    fill: rgb(255,255,255);
+    stroke: rgb(255,255,255);
+    color: rgb(255,255,255);
+}
+
 """
 
 TEMPLATE = """
@@ -137,7 +158,7 @@
 <title> 
 {title}
 </title>
-
+<link rel="stylesheet" href="http://www.eleves.ens.fr/home/doulcier/projects/math/nv.d3.css"></link>
 <style>
 {css}
 </style>
@@ -156,6 +177,50 @@
 </html>
 """
 
+SCRIPT ="""
+
+<script src="http://www.eleves.ens.fr/home/doulcier/projects/math/d3.v3.js"></script>
+<script src="http://www.eleves.ens.fr/home/doulcier/projects/math/nv.d3.min.js"></script>
+
+<script>
+var data = {data}
+nv.addGraph(function() {{
+  var chart = nv.models.stackedAreaChart()
+                .x(function(d) {{ return d[0] }})
+                .y(function(d) {{ return d[1] }})
+                .clipEdge(true)
+                .useInteractiveGuideline(true)
+                ;
+
+  chart.xAxis
+      .showMaxMin(false)
+;
+
+  chart.yAxis
+      .tickFormat(d3.format(',.2f'));
+
+  d3.select('#chart svg')
+    .datum(data)
+      .transition().duration(500).call(chart);
+
+  d3.selectAll('#chart svg text')
+     .style('fill','#839496');
+
+  d3.selectAll('#nv-controlsWrap')
+     .style('display','None');
+
+
+
+  nv.utils.windowResize(chart.update);
+
+  return chart;
+}});
+
+
+
+</script>
+"""
+
 FOOTER = '<a href="http://www.gt-mathsbio.biologie.ens.fr/">GT-MathsBio </a> -- Page generated on the {date} by <a href="https://github.com/geeklhem/ipdt"> ipdt</a>.'
 
 class HTMLexporter(object):
@@ -173,7 +238,7 @@ def __init__(self,path,ranking,payoff_matrix,param,info_strategies):
         self.sections = [
             ("info","Informations",self.general_info(param)),
             ("ranking","Ranking",self.ranking(ranking,info_strategies)),
-            ("details","Detailed Results",self.details(ranking, payoff_matrix,
+            ("details","Detailed Results",self.details(zip(*ranking)[1], payoff_matrix,
                                                        info_strategies, param)),
         ]
 
@@ -208,19 +273,18 @@ def general_info(self,param):
 
 
     def get_color(self,score,param):
-        diff = sorted([(abs(score-param[m]*param["T"]),m)
+        diff = sorted([(abs(score-param[m]*param["T"]*param["replicas"]),m)
                        for m in ["cc","dc","cd","dd"]],
                       key=lambda x:x[0])
         return(self.move_color[diff[0][1]])
 
-    def details(self,ranking,po,info,param):
+    def details(self,order,po,info,param):
         s = '<table border="0" cellpadding="3" cellspacing="3">\n<tr><th></th>\n'
-        order = zip(*ranking)[1]
 
         max_po = max([max(po[k].values()) for k in order])
         min_po = min([min(po[k].values()) for k in order])
 
-        norm = lambda x: int(100*(x - min_po) / (max_po-min_po)) 
+        norm = lambda x: int(100*(x - min_po) / (max_po-min_po)) if (max_po-min_po) else x
 
         if len(order)>5:
             for n,k in enumerate(order) :
@@ -259,17 +323,17 @@ def ranking(self,ranking,info):
         for score,code in ranking:
             s+= ("<li><strong title=\"{3}\">{1}</strong> "
                  "(<em>{2}</em>) - {0} pts </li>\n").format(score,
-                                                          info[code]["name"],
-                                                          info[code]["author"],
-                                                          info[code]["description"])
+                                                            info[code]["name"],
+                                                            info[code]["author"],
+                                                            info[code]["description"])
         s += "</ol>\n"
         s += "<em>(Do a mouseover on the name of each strategy to get a short description.)</em>"
         return s
 
     def output(self):
         body = ""
         for code,title,text in self.sections:
-            body += "\n\n<div id='{}'><h2>{}</h2></div>\n{}".format(code,title,text)
+            body += "\n\n<div id='{}'><h2>{}</h2>\n{}\n</div>".format(code,title,text)
         footer =  FOOTER.format(date=time.asctime())
         out = TEMPLATE.format(body=body, css=CSS, title="ipdt report",footer=footer)
         return out 
@@ -278,6 +342,45 @@ def save(self):
         with open(self.path,'w') as f:
             f.write(self.output())
 
+
+
+class HTMLexporterTS(HTMLexporter):
+    def __init__(self,path,time_series,payoff_matrix,param,info_strategies):
+        self.path = path
+
+        moves = sorted([(move, param[move]) for move in ["cc","dc","cd","dd"]],
+                       key=lambda x:-x[1])  
+        colors = ['class="green"','class="blue"','class="yellow"','class="red"']
+        self.move_color = {}
+        for n,move in enumerate(moves):
+            self.move_color[move[0]] = colors[n] 
+
+
+        self.sections = [
+            ("info","Informations",self.general_info(param)),
+            ("ts","Time series",self.time_series_d3(time_series,info_strategies)),
+            ("details","Detailed Results",self.details(time_series.keys(), payoff_matrix,
+                                                       info_strategies, param)),
+        ]
+
+    def time_series_d3(self,time_series,info):
+        data = "[\n"
+        offset =  None
+        for k,v in time_series.items():
+            values = []
+            if offset is None:
+                offset =  [0]*len(v)
+            for j,p in enumerate(v):
+                values.append([j,p])
+                offset[j] += p
+            data += '{{ "key": "{}", "values":{}}},'.format(k,values)
+
+        data += "]\n"
+        s = SCRIPT.format(data=data)
+        s += '<div id="chart"> <svg></svg> </div>'
+        return s
+
+
 if __name__ == "__main__":
     from ipdt.tournament import DEFAULT_PARAM as param
     a = HTMLexporter("test.html",
@@ -292,3 +395,5 @@ def save(self):
                          "naivecoop":{"name":"Naive cooperator","author":"Axelrod"}
                      })
     a.save()
+
+