Species richness test vascular plants

[samaperrin]

Why have changes been made?

@PhilipMostert has created a version of the intSDM package which can produce a species richness estimation and a sampling bias estimation per taxa. This needs to be integrated into the pipeline.

What changes have been made?

• pipeline/models/speciesModelRuns.R - This script now has several adaptations that allow different inputs to the iSDM based on the variable 'modelRun'. The modelResultsCOmpilation.R script has also been removed and now stands on its own in the master script.
• masterScript.R - You now need to define which type of model you are running here. SMall variable changes have been made, and the modelResultsCompilation script also needs to be run separately.
• pipeline/models/utils/modelResultsCompilation.R - Since this script doesn't actually create any results, only prepares them for the Hotspsots app, this has been separated from the speciesModelRuns script and can be run optionally for whatever date's results should be delivered to the Hotspots app.
• functions/refineSpeciesData.R - This filters our speciesData file based on the modelRun variable. For the richness model it gets rid of all absences, for the redListRichness model it gets rid of all absences and filters down to only red-listed species, for the red listed individual species models it cuts down to red listed species that have over a certain threshold of observations.
• functions/createPredictionData.R - This creates a series of points to project our predictions onto
• data/run_2024-01-05 - New data run (vascular plants in Trøndelag)

Minor related bug fixes:

• functions/modelPreparation.R - Had the wrong name for focalTaxon in here
• functions/processFieldNotesEvent.R - Remove invalid species from data

[RRTogunov]

Can't seem to debug this last error that comes up in sdmWorkflow():

>   sdmWorkflow(workflow, predictionData = predictionData)
Error in str2lang(x) : <text>:1:676: unexpected input
1: = "linear") + Malus_sylvestris_aspect(main = Malus_sylvestris_aspect, model = "linear") + Taxus_baccata_aspect(main = Taxus_baccata_aspect, model = "linear") + Trifolium_fragiferum_aspect(main
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ^

[samaperrin]

Can't seem to debug this last error that comes up in sdmWorkflow():

>   sdmWorkflow(workflow, predictionData = predictionData)
Error in str2lang(x) : <text>:1:676: unexpected input
1: = "linear") + Malus_sylvestris_aspect(main = Malus_sylvestris_aspect, model = "linear") + Taxus_baccata_aspect(main = Taxus_baccata_aspect, model = "linear") + Trifolium_fragiferum_aspect(main
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ^

So I got this a while back too, and managed to remove it by getting rid of any weird characters that were hanging around. The speciesDataProcessing.R script should take care of this though when it defines "simpleScientificName". Maybe double check the names and see if there's an errant special character that's snuck in? For me it was a tiny 'x' in hybrid species name