Select species based on model diagnostics
selectSppFromDiag.Rd
The datapipeline produces one occupancy diagnostic file for each species and year. This function combines all these files and returns those species with convergence or goodnes-of-fit issues.
Usage
selectSppFromDiag(config, sp_codes, year, module = c("dst", "abu"))
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.
- module
Either "dst" if we want occupancy diagnostics or "abu" if we want state-space model diagnostics.
Value
A list with two elements: $no_converge, contains codes of all species with convergence issues, $bad_fit, contains codes of species with goodness-of-fit issues (small Bayesian p-value).
Examples
if (FALSE) { # \dontrun{
config <- configPipeline(year = 2010,
dur = 3,
occ_mod = c("log_dist_coast", "elev", "log_hum.km2", "wetcon",
"watrec", "watext", "log_watext", "watext:watrec",
"ndvi", "prcp", "tdiff"),
det_mod = c("(1|obs_id)", "log_hours", "prcp", "tdiff", "cwac"),
fixed_vars = c("Pentad", "lon", "lat", "watocc_ever", "wetext_2018","wetcon_2018",
"dist_coast", "elev"),
package = "spOccupancy",
data_dir = "analysis/hpc/imports",
out_dir = "analysis/hpc/imports",
server = TRUE)
sp_codes <- config$species
selectSppFromDiag(config, sp_codes, 2008)
} # }