Merge branch 'master' of https://github.com/hzi-bifo/Phylogeography_P…

…aper

README.md

@@ -22,6 +22,6 @@ This folder contains all codes for:
 
 For details stating dependencies, necessary input files as well as instructions how to run the software, please see the [readme for the simulation](https://github.com/hzi-bifo/Phylogeography_Paper/blob/master/Software/Simulation/README.md) as well as the [readme for the reconstruction](https://github.com/hzi-bifo/Phylogeography_Paper/blob/master/Software/Reconstruction/README.md).
 
-The distance matrices used for the parsimonious reconstruction can be found at TODO: ADD ZENODO LINK WHEN ONLINE
+The distance matrices used for the parsimonious reconstruction can be found [in this data repository](https://zenodo.org/record/2643163#.XMqf4kNS-EI).
 
 Software for the comparison of the reconstructed spread to the simulated one can be found in the [FrechetTreeDistance repository](https://github.com/hzi-bifo/FrechetTreeDistance).

Software/Reconstruction/README.md

@@ -15,13 +15,14 @@ Input arguments are:
 The script can be called via:
 > Rscript phylogeo_sankoff.R \[tree\] \[locations\] \[distance matrix\] \[output\]
 
-For example, to perform the reconstruction for the first simulation in the study using effective distances and airports as possible locations:
+To test the software on the artificial, minimal example shown in Figure 1 of the manuscript and provided here as testdata, open this folder on the command line and run it via:
+> Rscript phylogeo_sankoff.R testdata/tree.phy testdata/tipdata.txt testdata/distance.matrix.csv testdata/reconstruction
+
+Otherwise, to perform the reconstruction for the first simulation in the study using effective distances and airports as possible locations:
 > Rscript phylogeo_sankoff.R ../../Data/Simulations/Sim_1/simulated_seq_cds.labeled.phy ../../Data/Simulations/Sim_1/tipdata.txt /path/to/effective.distance.matrix.csv reconstruction_effective
 
-The output files are:
+Distance matrices can be downloaded from [this data repository](https://zenodo.org/record/2643163#.XMqf4kNS-EI).
+
+The output files created by the reconstruction are:
 * \[output\].phy: the phylogenetic tree with added (or overwritten if previously available) node labels
 * \[output\].annotation.phy: a tab-separated text file stating the labels and the observed and reconstructed locations for all tips and internal nodes
-
-## Evaluation pipeline
-
-todo