Man pages for PacificCommunity/ofp-sam-diags4MFCL
R functions for presenting MULTIFAN-CL results and diagnostics

colour.palettesModel palettes
length.fit.preparationRead in and process length.fit file
likelihood.tableTable of likelihood components
par-methodsjitter
plot.age.distPlot the distribution an age class by region and quarter
plot.biomassCompare the estimated biomass across different models.
plot.biomass.contributionsPlot the contributions to biomass from each region Original...
plot.comparisonsWrapper function for plotting model comparisons
plot.depletionCompare the estimated depletion across different models.
plot.effort.dev.penaltiesPlot effort deviation penalties over time by fishery and...
plot.effort.devsPlot effort deviations over time by fishery
plot.everythingCreate all of the diagnostic plots from a given directory
plot.frqitPlot a frqit::frq object
plot.F.temporalCompare the fishing mortality across different models.
plot.growthCompare the estimated growth across different models. If...
plot.kobeKobe plot
plot.len.wt.temporalPlot the temporal change in median length and weight of...
plot.likelihood.profilesPlot the likelihood profiles
plot.majuroMajuro plot
plot.maturityPlot maturity for each model give choice of by length or age
plot.movement.matrixPlot the movement esimated movement for a single MFCLPar or...
plot.nat.mortPlot natural mortality of each model
plot.overall.composition.fitPlot composite catch-at-length data for each fishery.
plot.pred.obs.catchPlot difference between observed and predicted catches
plot.pred.obs.cpuePlot time series of the predicted and observed CPUE for...
plot.rec.devsPlot estimated recruitment deviates
plot.rec.distPlot recruitment distribution proportions
plot.rec.dist.decadePlot recruitment distribution proportions by decade for a...
plot.selectivityCompare the estimated selectivity across different models.
plot.srrPlot the stock-recruitment relationship
plot.tag.attritionPlot the observed and predicted tag attrition.
plot.tag.reporting.ratesPlot the tag reporting rates
plot.tag.return.proportionPlot proportions of tag returns by region
plot.tag.returns.timePlot the observed and predicted tag recaptures.
status.tableTable of stock status metrics
tag.data.preparationPrepare data for tagging plots
PacificCommunity/ofp-sam-diags4MFCL documentation built on July 23, 2020, 11:24 p.m.