diag_temp_thresholds: Compares the temperature forcing data to the Group...

In sgaichas/atlantisdiagnostics: Process Atlantis model output and implements model performance diagnostics

Compares the temperature forcing data to the Group temperature thresholds

Description

Determine if Groups have suitable habitat based on temperature thresholds. Horizontal redistribution proportions (FXXX_SY and recruit_hdist) and vertical distributions (vertDAY,vertNIGHT, recruit_vdistrib) are used to identify the spatial extent of the groups. Groups are then assessed as to whether these polygons are considered habitable based on temperature.

Note: The union of polygons over all seasons is used in comparisons

Usage

diag_temp_thresholds(paramList, speciesCodes = NULL)

Arguments

paramList	A list of parameter files (Output of get_atl_paramfiles())
speciesCodes	A character string of the species/group name of interest. Default is NULL (All species)

Value

A data frame. Only groups that fail are returned. The columns are:

group	Species/Group name
layer	Polygon layer
recruitBoxes	Proportion of boxes that are not habitable for recruits due to temperature (relative to defined range)
ageBoxesAdult	Proportion of boxes that are not habitable for adults due to temperature (relative to defined range)
ageBoxesJuv	Proportion of boxes that are not habitable for juveniles due to temperature (relative to defined range)
recruitTime	Proportion of time in model that recruits were distributed away from non habitable polygons
ageTimeAdult	Proportion of time in model that adults were distributed away from non habitable polygons
ageTimeJuv	Proportion of time in model that juveniles were distributed away from non habitable polygons
pass	Logical indicating if the species passes the temperature threshold test. All fields < 0.01

Layers

1 = Surface, n is sediment The sediment layer is not returned in the output.

See Also

Other diagnostics: diag_cohortBiomass(), diag_fleet_catch(), diag_footprints(), diag_maxsize(), diag_persistence(), diag_reasonability()

Examples

## Not run: 
# Declare paths to files required
paramList <- list()
paramList$bgm.file <- "Full path to bgm file"
paramList$biol.prm <- "Full path to biology prm file"
paramList$run.prm <- "Full path to run prm file"

# check for any species that maybe impacted by temperature
diag_temp_thresholds(paramList,speciesCodes=NULL)

# check for HERRING and WHITE HAKE
diag_temp_thresholds(paramList,speciesCodes=c("HER","WHK"))

## End(Not run)

sgaichas/atlantisdiagnostics documentation built on June 13, 2025, 6:11 a.m.