We have a new model format and outputs, and as such there is a lot of debugging to be done, particularly in the model results compilation. Additionally, there's a new run attached here, with vascular plant results for Trondheim (but only for red listed richness, NOT all species richness).
What changes have been made?
functions/defineBiasFields.R - For our red listed richness modelling, this was discarding datasets that didn't have any valid (ie. more than x observations) red listed species in them - this is only a filter to be used for individual models.
functions/modelPreparation.R - This function was filtering datasets to be used in model runs, which is now taken care of by the refineSpeciesData() function
masterScript.R - Stupid spelling mistake here
pipeline/import/taxaImport.R - No longer any need to export data straight to visualisation folder - we do this at the end now (IF we want to)
pipeline/models/speciesModelRuns.R - Various fixes here. Red list needed to be explicitly defined for the "defineBiasFields" model so that it didn't do any unwanted filtering when we were looking at all species richness. The rename of richness and bias predictions to end with "Preds.rds" was encessary since the species model compiler searches for files ending with "Predictions.RDS" and thus was picking up the richness and bias files too. dateAccessed is now a necessity for this script.
pipeline/models/utils/modelResultsCompilation.R - Rewrite to account for new data, and new data structure.
Why have changes been made?
We have a new model format and outputs, and as such there is a lot of debugging to be done, particularly in the model results compilation. Additionally, there's a new run attached here, with vascular plant results for Trondheim (but only for red listed richness, NOT all species richness).
What changes have been made?