Creates post-processing output for Atlantis
Usage
process_atl_output(
param.dir,
atl.dir,
out.dir = file.path(atl.dir, "Post_Processed/Data/"),
run.prefix,
param.ls,
agg.scale = "day",
large.file = F,
system,
process.all = F,
plot.all = F,
plot.benthic = F,
plot.overall.biomass = F,
plot.biomass.timeseries = F,
plot.length.age = F,
plot.biomass.box = F,
plot.c.mum = F,
plot.sn.rn = F,
plot.recruits = F,
plot.numbers.timeseries = F,
plot.physics = F,
plot.growth.cons = F,
plot.cohort = F,
plot.diet = F,
plot.consumption = F,
plot.spatial.biomass = F,
plot.spatial.biomass.seasonal = F,
plot.catch = F,
plot.catch.fleet = F,
plot.spatial.catch = F,
plot.mortality = F,
plot.weight = F,
plot.spatial.overlap = F
)Arguments
- param.dir
string. Path to location of atlantis parameter files
- atl.dir
string. path to location of atlantis output files
- out.dir
string. path to desired location of post-processed output
- run.prefix
string. Prefix for atlantis run output (specified in runcommand.bat)
- param.ls
list generated from get_atl_paramfiles()
- agg.scale
Scale to aggregate dietcheck biomass from (either 'raw','month', or 'year' )
- large.file
Boolean.
- system
String. "Windows" or "Linux"
- process.all
Boolean. Global option to process all components
- plot.all
Boolean. Global flag for plotting everything
- plot.benthic
logical. Benthic plots show timeseries of all benthic and epibenthic groups for one box
- plot.overall.biomass
logical. Plots showing the total biomass across all functional groups as stacked barplots
- plot.biomass.timeseries
logical. Plots showing biomass-related timeseries on various aggregations and reference points
- plot.length.age
logical. Plots relating to the length-age relationship of age-structured groups
- plot.biomass.box
logical. Plots relating to biomass but grouped by box
- plot.c.mum
logical. Plots and tables related to tuning C and mum parameters
- plot.sn.rn
logical. Plots relating to SN and RN timeseries
- plot.recruits
logical. Plots of recruitment and SSB timeseries
- plot.numbers.timeseries
logical. Plots showing timeseries of numbers (as opposed to biomass)
- plot.physics
logical. Plots of physical statevariables as well as fluxes
- plot.growth.cons
logical. Plots relating to growth and consumption
- plot.cohort
logical. Plots showing timeseries of each cohort across age-structured groups
- plot.diet
logical. Plots showing predation of and consumption by each functional group
- plot.consumption
Boolean. Plots showing consumption
- plot.spatial.biomass
logical. Plots showing the spatial (box/level) structure of groups' biomass
- plot.spatial.biomass.seasonal
logical. Plots showing the spatial (box/level) structure of groups' biomass
- plot.catch
logical. Plots annual catch(mt) age based catch (numbers) and age based %ages
- plot.catch.fleet
Boolean
- plot.spatial.catch
logical. Plots showing the spatial (box/level) structure of groups' catch
- plot.mortality
logical. Plots Mortality (F, M1, M2) from two output sources (Mort, SpecificMort)
- plot.weight
logical. Plots the maximum size of fish in each size class over the domain
- plot.spatial.overlap
Boolean