Sorghum VPD covariate winnowing

genophenoenvo / terraref-datasets

Repository for code and small datasets derived from the TERRA REF program

MIT License

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Sorghum VPD covariate winnowing #108

Closed rbartelme closed 3 years ago

rbartelme commented 4 years ago

PCA may not be the best approach for this.

[x] Meet with @dlebauer about methods to find covariates of vpd at all sites
[x] choose appropriate method for finding covariation
[x] Report variables independent of VPD (ex. Temp and RH will not be independent)
[x] Adjust network model features according to variable independence

rbartelme commented 4 years ago

Also changed sprint/points of this task and made a more granular task list, as well as updated title.

rbartelme commented 4 years ago

Re-Do PCA for canopy height ~ variables and report the percent variation explained by each component.

rbartelme commented 4 years ago

Centered and scaled PCA of all sites' combined: canopy heights, and all environmental variables.

rbartelme commented 4 years ago

Centered and scaled PCA of all sites' combined: canopy heights, vpd mean, gdd, and cumulative precipitation.

rbartelme commented 4 years ago

It seems that cumulative precipitation, some min/median/max vpd, and derivations from the canopy_height ~ gdd growth curve could work well in the context of the network. The new tabular input colnames would be something like:

cultivar experiment``growth_rate growth_maximum days_to_flowering days_to_flag_leaf_emergence vpd_param cum_precip

It could be worth adding inbreeding_coefficient for each cultivar?? as a genetic data product??