DACE User Acceptance Tests

Data upload and preparation

1. Anna wants to load the tree file in newick format
   1. files: aquilegia-tree.txt, DsetH1.phy, Lobelioids-tree.txt
   2. expected 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: aquilegia.nex
   2. expected results: as in 1
3. Anna wants to load the data table in csv format
   1. files: aquilegia-traits.txt, DsetH1.csv, Lobelioids-traits-disc.csv, Lobelioids-traits-disc2.csv, Lobelioids-traits-disc3.csv
   2. expected results: data table correctly loaded
4. Anna wants to load the data table in nexus format
   1. file: aquilegia.nex
   2. expected 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, name paired (Lobelioid-tree.txt can be paired with Lobelioids-traits-disc.csv, Lobelioids-traits-disc2.csv and Lobelioids-traits-disc3.csv).
   2. expected results: all PASS
6. Anna wants to be able to review and modify the matches
   1. see 5

Analysis and results

1. Anna wants to know the proportional likelihoods of the different states of a discrete trait at the internal nodes of the tree
   1. expected results: all PASS
2. Anna wants to be able to download the computed likelihoods (nodes.txt)
3. Anna needs a way to match the likelihoods to the internal nodes (tree.txt)
4. Anna wants to visualize the likelihoods on her tree (plot.pdf)
5. Anna wants to estimate the rate of evolution of that trait and the associate measure of uncertainty (out.txt)
6. Anna wants to obtain a likelihood for her model (out.txt)
   1. 2-6, see respective Results folders
7. Anna wants to repeat the same analysis with a different starting parameter
   1. files: aquilegia-tree.txt, aquilegia-traits.txt. Starting parameter: IP=1.3
   2. expected results: PASS, as in Aquilegia/Repeat

Dataset

dace_test.gz