Save index model outputs to disk

A convenience wrapper that takes the outputs from run_sdmtmb(), diagnose(), and calc_index_areas() when run with dir = NULL and writes them all to disk in the same directory structure as the original indexwc code.

save_index_outputs(
  fit,
  diagnostics,
  indices,
  dir = getwd(),
  dir_main = lifecycle::deprecated(),
  overwrite = FALSE
)

Arguments

fit

An sdmTMB model object returned by run_sdmtmb() with dir = NULL

diagnostics

A list returned by diagnose() with dir = NULL

indices

A list returned by calc_index_areas() with dir = NULL

dir

A string specifying a path where results will be saved. The default is your current working directory. A subdirectory structure will be created based on the species, survey, and model family. If NULL, the fitted object is returned with nothing saved to disk

dir_main

Deprecated. A string specifying a path where results will be saved. The default is your current working directory. A subdirectory structure will be created based on the species, survey, and model family. If NULL, the fitted object is returned with nothing saved to disk

overwrite

Logical. If TRUE, existing files will be overwritten. Default is FALSE

Details

This function recreates the file structure that would have been created if you had run run_sdmtmb(), diagnose(), and calc_index_areas() with directory arguments specified from the start.

The directory structure created is:

dir/
└── species_name/
    └── survey_name/
        └── family_name/
            ├── data/
            │   ├── data.rdata
            │   └── fit.rds
            ├── diagnostics/
            │   ├── mesh.png
            │   ├── sanity_data_frame.csv
            │   ├── aic_nll.txt
            │   ├── run_diagnostics_and_estimates.rdata
            │   ├── qq.png
            │   ├── residuals_1_*.png
            │   ├── residuals_2_*.png (if delta model)
            │   ├── anisotropy.png
            │   ├── fixed_effects.png
            │   ├── density_*.png
            │   ├── data_with_residuals.rdata
            │   └── predictions.rdata
            └── index/
                ├── est_by_area.csv
                ├── index_coastwide.png (if Coastwide calculated)
                └── index_all_areas.png

See also

• run_sdmtmb(), fit the model

• diagnose(), run diagnostics

• calc_index_areas(), calculate indices

Author

Chantel R. Wetzel

Examples

if (FALSE) { # \dontrun{

# Pull and format data
my_data <- pull_and_format_data(
   configuration_to_run = configuration[1,]
)

# Fit model without saving
fit <- run_sdmtmb(
  data = my_data$data_filtered,
  family = my_data$family,
  formula = my_data$formula
)

# Run diagnostics without saving
diag <- diagnose(
  fit = fit
)

# Calculate indices without saving
index <- calc_index_areas(
  data = fit$data,
  fit = fit,
  boundaries = "Coastwide"
)

# Now save everything to disk
paths <- save_index_outputs(
  fit = fit,
  diagnostics = diag,
  indices = index,
  dir = fit$dir
)
} # }