Compares the temperature forcing data to the Group temperature thresholds
Source:R/diag_temp_thresholds.R
diag_temp_thresholds.Rd
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
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
See also
Other diagnostics:
diag_cohortBiomass()
,
diag_fleet_catch()
,
diag_footprints()
,
diag_maxsize()
,
diag_persistence()
,
diag_reasonability()
Examples
if (FALSE) { # \dontrun{
# 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"))
} # }