| R/atlantis_tracer.R {mfdbatlantis} | R Documentation |
Routines to read and make use of the tracer output files
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)
atlantis_tracer_survey_select(
tracer_data,
length_group,
survey_suitability,
survey_sigma)
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 |
survey_suitability |
Sutiability for vessel per-length-group |
survey_sigma |
Error rate per-length-group |
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.