DACE User Acceptance Tests
Data upload and preparation
- Anna wants to load the tree file in newick format
- files: aquilegia-tree.txt, DsetH1.phy, Lobelioids-tree.txt
- expected results: corresponding .pdf files for reference. File with ###_c.pdf: tree image with branch lengths, ###_p.pdf: tree image without branch lengths
- Anna wants to load the tree file in nexus format
- files: aquilegia.nex
- expected results: as in 1
- Anna wants to load the data table in csv format
- files: aquilegia-traits.txt, DsetH1.csv, Lobelioids-traits-disc.csv, Lobelioids-traits-disc2.csv, Lobelioids-traits-disc3.csv
- expected results: data table correctly loaded
- Anna wants to load the data table in nexus format
- file: aquilegia.nex
- expected results: data table correctly loaded
- Anna wants to automatically match the taxa names in the table to the taxa names in the tree
- 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).
- expected results: all PASS
- Anna wants to be able to review and modify the matches
- see 5
Analysis and results
- Anna wants to know the proportional likelihoods of the different states of a discrete trait at the internal nodes of the tree
- expected results: all PASS
- Anna wants to be able to download the computed likelihoods (nodes.txt)
- Anna needs a way to match the likelihoods to the internal nodes (tree.txt)
- Anna wants to visualize the likelihoods on her tree (plot.pdf)
- Anna wants to estimate the rate of evolution of that trait and the associate measure of uncertainty (out.txt)
- Anna wants to obtain a likelihood for her model (out.txt)
- 2-6, see respective Results folders
- Anna wants to repeat the same analysis with a different starting parameter
- files: aquilegia-tree.txt, aquilegia-traits.txt. Starting parameter: IP=1.3
- expected results: PASS, as in Aquilegia/Repeat
Dataset
dace_test.gz
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