CACE User Acceptance Tests

Data upload and preparation

1. Anna wants to load the tree file in newick format
   1. files: acer-tree.txt, aesculus-tree.txt, arctostaphylos-tree.txt, CsetH1.phy
   2. results: corresponding .pdf files for reference. File with ###_c.pdf: tree image with branch lengths, ###_p.pdf: tree image without branch lengths
2. Anna wants to load the tree file in nexus format
   1. files: acer.nex, arctostap.nex
   2. results: as in 1
3. Anna wants to load the data table in csv format
   1. files: acer-traits.csv, aesculus-traits.csv, arctostaphylos-trait.txt, CsetH1.csv
   2. results: data table correctly loaded
4. Anna wants to load the data table in nexus format
   1. files: acer.nex, aesculus.nex, arctostaphylos.nex
   2. results: data table correctly loaded
5. Anna wants to automatically match the taxa names in the table to the taxa names in the tree
   1. files: all the above, paired.
   2. results: acer, arctostap, CsetH1: PASS; aesculus: FAIL
6. Anna wants to be able to review and modify the matches
   1. files: aesculus-tree.txt, aesculus-traits.csv.
   2. result: matched dataset as in Aesculus/matched/

Analysis and results

1. Anna wants to estimate the trait values at the internal nodes of the tree and their associated uncertainties
   1. acer: FAIL
   2. aesculus: PASS (depends on 6b), results as in Aesculus/matched
   3. arctostap: PASS
   4. CsetH1: PASS
2. Anna wants to be able to download the computed values (nodes.txt)
3. Anna needs a way to match the values to the internal nodes (tree.txt)
4. Anna wants to visualize the values on her tree (plot.pdf)
5. Anna wants to obtain a likelihood for her model (out.txt)
   1. 2-5, see respective Results folders

Dataset

cace_test.gz