plot gadget fit

Plot Gadget fit

# S3 method for gadget.fit
plot(x, ...)

Arguments

x

results from gadget fit

...

Can include

type

The type of plot that is returned, depends on the input data (see details)

data

What results should be plotted, default sidat

Value

ggplot2::ggplot object

Details

Plot the results from gadget.fit. The function produces a different plots by datatype and plottype. Valid datatypes are:

sidat

Surveyindices

summary

Likelihood summary data

catchdist.fleets

Catchdistribution data

stockdist

Stockdistribution data

res.by.year

Results by year

stock.std

Age composition from the model

suitability

Suitability estimated from the model by year and step

params

Parameter values relative to their boundaries

and valid plottypes are:

direct

Default value, plots direct comparisons of data with model output. Valid for all datatype except 'res.by.year'

weighted

Only for 'summary'. Plots the weighted likelihood value for each component.

pie

Only for 'summary'. Plots the likelihood composition as a pie chart

lengths

Only for 'sidat'. Plot the surveyindex based on the SI length group instead of component name.

bio

Only for 'sidat'. Plot the biomass weighted survey index, assumes length based abundance index.

x-y

Only for 'sidat'. Produces a x-y scatter-plot for the fitted and observed index.

resid

Only for 'catchdist.fleets'. Produces a residual plot for each component.

bubble

Only for 'catchdist.fleets'. Produces a bubble plot for each component.

growth

Only for 'catchdist.fleets'. Produces a plot of fitted growth for each age-length component.

resid

Only for 'catchdist.fleets'. Produces a residual plot for each component.

F

Only for 'res.by.year'. Produces a F plot by stock.

total

Only for 'res.by.year'. Produces a total biomass plot by stock.

catch

Only for 'res.by.year'. Produces a total catch plot by stock.

rec

Only for 'res.by.year'. Produces a recruitment biomass plot by stock.

Author

Bjarki Þór Elvarsson

Examples

if (FALSE) {
## collect the data from gadget
fit <- gadget.fit()
## plot survey indices
plot(fit) 
## plot likelihood
plot(fit,data='summary')
}