Include new example.

trvrb · Feb 24, 2014 · 595bd8d · 595bd8d
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diff --git a/README.md b/README.md
@@ -45,10 +45,10 @@ The simulation will output a timeseries of region-specific prevalence and incide
 [`out.timeseries`](example/out.timeseries).  It will also sample viruses periodically and output their 
 geographic and antigenic locations to [`out.tips`](example/out.tips) and a tree connecting these samples 
 to [`out.branches`](example/out.branches).  This file contains pairs of viruses, child and parent, 
-representing nodes in a genealogy.
+representing nodes in a genealogy.  Average values are output to [`out.summary`](example/out.summary).
 
 If you have Mathematica, you can generate a number of figures from this output by running the
-notebook [`antigen-analysis.nb`](antigen-analysis.nb).
+notebook [`antigen-analysis.nb`](example/antigen-analysis.nb).
 
 ## Memory
 

diff --git a/antigen-analysis.nb b/antigen-analysis.nb
diff --git a/example/README.md b/example/README.md
@@ -0,0 +1,61 @@
+## Timeseries
+
+### Prevalence
+
+![](prevalence.png)
+
+![](prevalenceSpatial.png)
+
+### Incidence
+
+![](incidence.png)
+
+![](incidenceSpatial.png)
+
+### Diversity
+
+![](diversity.png)
+
+![](diversitySpatial.png)
+
+### TMRCA
+
+![](tmrca.png)
+
+![](tmrcaSpatial.png)
+
+## Virus samples
+
+### Map
+
+![](mapClusters.png)
+
+### Distance from origin
+
+![](virusYearDistance.png)
+
+### Cluster turnover
+
+![](clusterTurnover.png)
+
+### Incidence by cluster
+
+![](incidenceClustersSpatial.png)
+
+## Tree
+
+## Tree with clusters
+
+![](treeClusters.png)
+
+## Tree with geography
+
+![](treeSpatial.png)
+
+## Time vs AG1
+
+![](treeYearAG1Clusters.png)
+
+## AG1 vs AG2
+
+![](treeAG1AG2Clusters.png)
diff --git a/example/antigen-analysis.nb b/example/antigen-analysis.nb
diff --git a/example/clusterTurnover.pdf b/example/clusterTurnover.pdf
diff --git a/example/clusterTurnover.png b/example/clusterTurnover.png
diff --git a/example/diversity.pdf b/example/diversity.pdf
diff --git a/example/diversity.png b/example/diversity.png
diff --git a/example/diversitySpatial.pdf b/example/diversitySpatial.pdf
diff --git a/example/diversitySpatial.png b/example/diversitySpatial.png
diff --git a/example/incidence.pdf b/example/incidence.pdf
diff --git a/example/incidence.png b/example/incidence.png
diff --git a/example/incidenceClustersSpatial.pdf b/example/incidenceClustersSpatial.pdf
diff --git a/example/incidenceClustersSpatial.png b/example/incidenceClustersSpatial.png
diff --git a/example/incidenceSpatial.pdf b/example/incidenceSpatial.pdf
diff --git a/example/incidenceSpatial.png b/example/incidenceSpatial.png
diff --git a/example/lagAG1Spatial.pdf b/example/lagAG1Spatial.pdf
diff --git a/example/mapClusters.pdf b/example/mapClusters.pdf
diff --git a/example/mapClusters.png b/example/mapClusters.png
diff --git a/example/netau.pdf b/example/netau.pdf
diff --git a/example/netauSpatial.pdf b/example/netauSpatial.pdf
diff --git a/example/out.branches b/example/out.branches
diff --git a/example/out.mk b/example/out.mk
diff --git a/example/out.range b/example/out.range
diff --git a/example/out.summary b/example/out.summary
@@ -0,0 +1,14 @@
+parameter	full
+diversity	2.2093
+tmrca	2.1013
+netau	10.7864
+serialInterval	0.01209
+antigenicDiversity	0.7292
+N	3000000.0000
+S	2996747.8140
+I	3252.1860
+R	0.0000
+cases	8128.7080
+sideBranchRate	0.7341
+trunkRate	1.5154
+mkRatio	2.0642
diff --git a/example/out.timeseries b/example/out.timeseries