Environment stratification tool#6093
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ryan-preble
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ryan-preble
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The tool works well and shows up properly on the job submissions table - good work!
It would also be good to add some lines to the tool compatibility function to display dataset compatibility with the analysis.
lukasmueller
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lukasmueller
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check comment about login requirement
:-)
| map => { 'application/json' => 'JSON' }, | ||
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| sub shared_phenotypes : Path('/ajax/environment_stratification/shared_phenotypes') : { |
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Should these functions be only available to logged in users?
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I have added dataset compatibility check plus login is required to use this tool. |
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| foreach my $analysis_name ("Dataset Analysis", "Environment Stratification") { |
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This is different from how all the other tools determine compatibility. It seems like this only requires a dataset to have trials and traits, but does not impose any requirement on the number of observed phenotypes. The other tools have a "warn" condition that explains the dataset meets the minimum requirements but may have low N, making results unreliable. The "dataset requirements" key is not present in any other tool. It is also unclear to me what the "Dataset Analysis" tool is and why it has the same requirements as environment stratification.
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I think this part should be flexible for breeders to decide how they are mounting the dataset to construct zones. They just need trials and at least a trait. Make it too restrict I think can cause more complains.
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Description
This PR adds the new Environment Stratification tool to Breedbase.
The tool allows users to select a dataset and trait, run environment stratification analysis, and review compatible environment groups based on genotype-by-
environment interaction. Results are returned through a new AJAX controller, processed by an R backend script, and displayed in a dedicated Mason/JavaScript
interface.
Main Features
ANOVA / Design Handling
The R script detects the available experimental design information and builds the ANOVA model accordingly.
Supported fixed-effect ANOVA structures include:
Row and column terms are only used when the trial design is explicitly row-column/spatial. They are ignored for CRD and RCBD even if coordinate columns are present.
Checklist
/t/data/fixture/patches/./docshas been updated./jsto/js/source/legacy.