Man pages for PacificCommunity/ofp-sam-diags4MFCL
R Functions for Presenting MULTIFAN-CL Results and Diagnostics
| colour.palettes | Model palettes |
| length.fit.preparation | Read in and process length.fit file |
| likelihood.table | Table of likelihood components |
| par-methods | jitter |
| plot.age.dist | Plot the distribution an age class by region and quarter |
| plot.biomass | Compare the estimated biomass across different models. |
| plot.biomass.contributions | Plot the contributions to biomass from each region Original... |
| plot.comparisons | Wrapper function for plotting model comparisons |
| plot.depletion | Compare the estimated depletion across different models. |
| plot.effort.dev.penalties | Plot effort deviation penalties over time by fishery and... |
| plot.effort.devs | Plot effort deviations over time by fishery |
| plot.everything | Create all of the diagnostic plots from a given directory |
| plot.frqit | Plot a frqit::frq object |
| plot.F.temporal | Compare Fishing Mortality Across Different Models |
| plot.growth | Compare the estimated growth across different models. If... |
| plot.kobe | Kobe plot |
| plot.len.wt.temporal | Plot the temporal change in median length and weight of... |
| plot.likelihood.profiles | Plot the likelihood profiles |
| plot.majuro | Majuro plot |
| plot.maturity | Plot maturity for each model give choice of by length or age |
| plot.movement.matrix | Plot the movement esimated movement for a single MFCLPar or... |
| plot.nat.mort | Plot natural mortality of each model |
| plot.overall.composition.fit | Plot composite catch-at-length data for each fishery. |
| plot.pred.obs.catch | Plot difference between observed and predicted catches |
| plot.pred.obs.cpue | Plot time series of the predicted and observed CPUE for... |
| plot.rec.devs | Plot estimated recruitment deviates |
| plot.rec.dist | Plot recruitment distribution proportions |
| plot.rec.dist.decade | Plot recruitment distribution proportions by decade for a... |
| plot.selectivity | Compare the estimated selectivity across different models. |
| plot.srr | Plot the stock-recruitment relationship |
| plot.tag.attrition | Plot the observed and predicted tag attrition. |
| plot.tag.attrition.v2 | Plot the observed and predicted tag attrition. |
| plot.tag.reporting.rates | Plot the tag reporting rates |
| plot.tag.return.proportion | Plot proportions of tag returns by region |
| plot.tag.return.proportion.v2 | Plot proportions of tag returns by region |
| plot.tag.returns.time | Plot the observed and predicted tag recaptures. |
| plot.tag.returns.time.v2 | Plot the observed and predicted tag recaptures. |
| status.table | Table of stock status metrics |
| tag.data.preparation | Prepare data for tagging plots |
| tag.release.data.preparation | Prepare tag release data for tagging plots |
