atlantis_tracer: Atlantis tracer parsers

In mareframe/mfdbatlantis: MareFrame Atlantis Interface

Description

Routines to read and make use of the tracer output files

Usage

atlantis_temperature(adir,
        area_data)
atlantis_fg_tracer(adir,
        area_data,
        fg_group,
        consumption = FALSE)
atlantis_tracer_add_lengthgroups(
        tracer_data,
        length_group,
        sigma_per_cohort
        keep_zero_counts = FALSE)
atlantis_tracer_survey_select(
        tracer_data,
        length_group,
        survey_suitability,
        survey_sigma)

Arguments

adir	The atlantis directory created by atlantis_directory
area_data	The area data returned by atlantis_read_areas
fg_group	One of the functional groups returned from atlantis_functional_groups
consumption	Include consumption data?
tracer_data	Output of atlantis_fg_tracer or atlantis_tracer_add_lengthgroups
length_group	Vector of c(min, min, min, ..., max) lengths
sigma_per_cohort	Vector of sigma per-cohort in age group
keep_zero_counts	Logical to indicate whether to keep areas with count of 0
survey_suitability	Suitability, 0..1 value for each length group to scale abundance
survey_sigma	Error rate per-length-group

Value

atlantis_temperature returns a data.frame of temperatures suitable for importing into MFDB.

atlantis_fg_tracer returns a data.frame containing total abundance/length/weight information, and optionally consumption/day for the given functional group. Can be imported into MFDB, but ideally a survey is simulated first.

atlantis_tracer_add_lengthgroups break up abundance from atlantis_fg_tracer into length groups, assuming a normal distribution around the Atlantis-reported mean.

atlantis_tracer_survey_select samples from atlantis_tracer_add_lengthgroups output based on the survey_suitability vector (possibly generated by rgadget), adding noise based on survey_sigma. The result is a data.frame that can be imported as a survey into MFDB.

mareframe/mfdbatlantis documentation built on May 21, 2019, 11:45 a.m.