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gjearevoll / BioDivMapping

A pipeline dedicated to analysing and visualising the biodiversity of different taxa in Norway
GNU General Public License v3.0
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taxa-specific covariate specification: in focalCovariates or focalTaxa? #115

Closed RRTogunov closed 6 months ago

RRTogunov commented 7 months ago

Regarding taxa-specific covariate specification, current approach utilises a "selected_speciesGroup" for each taxa in focalCovariates. However, I think it would be more intuitive to specify desired covariates as columns in focalTaxa rather than a column for each taxa in focalCovariates. I can see it being cumbersome to add/remove taxa columns in focalCovariates, especially if there are many taxa (eg, in another application of this pipeline, I have ~300 rows of "taxa" in focalTaxa). In contrast, as number of available covariates is relatively static, I think it is would be easier to specify covariates in focalTaxa.csv. The change would also replace the "selected_speciesGroup" syntax with covariate columns in focalTaxa with the same name as the covariates itself.

It's not a critical issue for me, so I default to what the majority think.

samaperrin commented 7 months ago

I agree with your suggestion that it should be in focal taxa

RRTogunov commented 7 months ago

linked to this, environmentalTaxa imports all covariates in all taxa, whether or not they are imported (eg if only modelling vascularPlants, but have specified "selected_fungi" in focalCovariates.CSV, all fungi covariates will be imported). https://github.com/gjearevoll/BioDivMapping/blob/281554e530c033f7e2650c78aec661c30b4bb413/pipeline/import/environmentalImport.R#L54