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Combine species occupancy diagnostics into a single object

combineOccuDiags.Rd

The datapipeline produces one occupancy diagnostic file for each species and year. This function reads diagnostics files and combines them into a single object

Usage

combineOccuDiags(config, sp_codes, year)

Arguments

config

A list with pipeline configuration parameters. See configPipeline.

sp_codes

SAFRING reference numbers of the species we want diagnostics for.

year

The year for which diagnostics are required.

Value

A dataframe with diagnostic paramters

Examples

if (FALSE) { # \dontrun{
config <- configPipeline(year = 2010,
                         dur = 3,
                         occ_mod = c("log_dist_coast", "elev", "log_hum.km2", "wetcon",
                                     "watrec", "watext", "log_watext", "watext:watrec",
                                     "ndvi", "prcp", "tdiff"),
                         det_mod = c("(1|obs_id)", "log_hours", "prcp", "tdiff", "cwac"),
                         fixed_vars = c("Pentad", "lon", "lat", "watocc_ever", "wetext_2018","wetcon_2018",
                                        "dist_coast", "elev"),
                         package = "spOccupancy",
                         data_dir = "analysis/hpc/imports",
                         out_dir = "analysis/hpc/imports",
                         server = TRUE)
sp_codes <- config$species

combineOccuDiags(config, sp_codes, 2008)
} # }