We are submitting a report to Milødirektoratet on the 20th of November. As such, a working version of the Shiny app with proper documentation and a reasonably intact file structure is a good idea. This has necessitated a lot of small changes and bug cleanups, as well as a new data run with Phil's improved intSDM changes.
What changes have been made?
data/external/focalCovariates.csv - focal covariates have been updated. Human density variables were giving lopsided maps and were removed. Variables which will be in some version of the final report were added.
data/run_2023-11-10/modelOutputs - new model outputs were created using a) new environmental covariates and b) updated modelling code pushed by Phil to intSDM
documentation/images - A series of images were uploaded to embellish our documentation pages
documentation - In-depth documentation for both the pipeline and the Shiny app were written and uploaded as R markdown documents
masterScript.R - A coarser mesh was created to improve runtime. Also, the threshold for number of observations to include a redlisted species for individual analysis can now be set in the master script.
pipeline/import/environmentalImport.R - Additional explanatory text was added, speciesData was removed as an import ( it isn't used) and a finer aggregation of environmental covariates for visualisation was implemented
pipeline/import/utils/defineEnvSource.R - A lower resolution is now used for human variables
pipeline/integration/speciesDataProcessing.R - The processed data list is no longer saved for visualisation as it it too large for an efficient Shiny app. Also, master script defined redListThreshold implemented.
pipeline/models/speciesModelRuns.R - Dimensions of outputs are now hard-coded into the script, giving higher resolution for prediction maps.
pipeline/models/utils/modelResultsCompilation.R - sf::st_transform was used instead of plotKML::reproject to account for new format of intSDM output
Substantial changes were also made to the Shiny app, including:
Redundant pages were removed
A metadata display was added
Covariate display names were updated
Tab names were updated
Image not available now displays for species for which iNatirualist could not provide a photo
Improved colour palettes are used for species maps
Why have changes been made?
We are submitting a report to Milødirektoratet on the 20th of November. As such, a working version of the Shiny app with proper documentation and a reasonably intact file structure is a good idea. This has necessitated a lot of small changes and bug cleanups, as well as a new data run with Phil's improved intSDM changes.
What changes have been made?
Substantial changes were also made to the Shiny app, including: