hotspots-of-change

Workflow (2) Analysis for Pteronura brasiliensis

For each species, the following order to run the code should be followed:

i. The first code to run is the pbrasiliensis_1_dataGeneration.qmd html. Four new files will be created:

• PA blobs for time1 and time2 (PA_species_time1_blobs and PA_species_time2_blobs).
• PO rasters for time1 and time2 (PO_species_time1_raster and PO_species_time2_raster).

ii. After, run pbrasiliensis_2_variableSelection.qmd html to get the best predictors for the modeled species. The predictors will be: cov.1, cov.2, cov.3, and cov.4.

iii. Then run the pbrasiliensis_3_dataPreparation.qmd html code with the selected predictors to prepare the data for the model. Four new files will be created:

• PO data for time1 and time2 (PO_pbrasiliensis_time1.model.data and PO_pbrasiliensis_time2.model.data).
• PA data for time1 and time2 (PA_pbrasiliensis_time1.model.data and PA_pbrasiliensis_time2.model.data).

iv. Run the model with pbrasiliensis_4_modelRun.qmd html. Two new files will be created:

• The JAGS model(pbrasiliensis_model.txt)
• The model output (pbrasiliensis_model.rds) - caution this is a >5GB file

v. And, finally, create the output figures with pbrasiliensis_5_modelOutputs.qmd html. The html output will show all the results, plus a new file will be created:

• The model diagnostics (docs/pbrasiliensis_model_diagnostics.pdf).

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