## Workflow for Calculating Scores

Install   You will not need to interact with or see the inside of ohicore during an assessment, but will need to install the software package only once at the start of the assessment, using devtools::install_github('ohi-science/ohicore').

Prepare Data   Prepare the data layers, scripting as much as possible in R, to aid transparency, reproducibility, and repeat or future assessments. See the Data for the Toolbox vignette for more detailed discussion of the data preparation process and recommendations.

Check Layers   Confirm the correct, most recent data layers are saved in the layers folder. Save them there if they are not there.

Register Data   Manually update layers.csv and scenario_data_years.csv. This consists of registering the data layers in the layers.csv, and updating information about alignment between scenario and data years in the scenario_data_years.csv.

Configure   Configure the toolbox by running ohicore::Conf, ohicore::CheckLayers, and ohicore::Layers.

Develop Models   Develop goal models in functions.R in the OHI assessment folder, running goal models line-by-line to confirm results make sense and functions act as expected.

Calculate Scores   Re-configure the toolbox once model development is complete, and calculate the scores by stepping through calculate_scores from the assessment repo!

## Calculating Scores

# run the configure_toolbox.r script to check configuration first
source('~/github/toolbox-demo/region2016/configure_toolbox.R')

# calculate scenario scores
scores <- ohicore::CalculateAll(conf, layers)

# save scores as scores.csv
write.csv(scores, 'scores.csv', na='', row.names = FALSE)