gadgetplots

Plot gadget3 model output using ggplot2. R package version 0.1.10

The gadgetplots package produces diagnostics graphics for gadget3 using ggplot2. The package replaces the plotting capabilities of Rgadget package which was designed to work with gadget2.

Installation

The gadgetplots is not available on CRAN yet. Use the devtools or remotes packages to install directly from GitHub:

# install.packages("devtools")
devtools::install_github("gadget-framework/gadgetplots")

Overview of plots

The package produces generally similar plots to Rgadget. Names and apperances of these plots have changed somewhat. There are two ways to produce the plots: either use a specific plot_*() or the generic plot() with param argument specifying the type of plot.

Load example data to demonstrate the plots:

library(gadgetplots)
data(fit) # Note that we'll need a better example dataset

Annual (ICES) plot

plot_annual(fit) # synonym: plot(fit)

Stock biomass and abundance

plot_biomass(fit, total = TRUE) # synonym: plot(fit, "total")

plot_biomass(fit, geom_area = TRUE) # synonym: plot(fit, "biomass", geom_area = TRUE)

plot_biomass(fit, biomass = FALSE) # synonym: plot(fit, "abundance")

Spawning stock

Currently requires definition of spawning stock among stocks in the gadget model (uses a reasonable guess: grep("fem.*mat")). Defining spawning stock based on length or age from the model is also possible, but needs to be implemented.

plot_ssb(fit) # synonym: plot(fit, "ssb")

Recruitment

plot_rec(fit) # synonym: plot(fit, "rec")

Fishing mortality (F)

plot_f(fit) # synonym: plot(fit, "f")

Modeled catches and harvest rate

plot_catch(fit, type = "stock") # synonym: plot(fit, "catch")

plot_catch(fit, type = "fleet") # synonym: plot(fit, "fleet")

plot_catch(fit, type = "hr") # synonym: plot(fit, "hr")

Survey indices

plot_si(fit) # synonym: plot(fit, "si")

Catch distribution

The function typically produces a list of plots. Here only one to save space

plot_catchdist(fit, name = "EggaN_ldist") # synonym: plot(fit, "catchdist")
#> $EggaN_ldist

Stock distribution

plot_stockdist(fit) # synonym: plot(fit, "stockdist")

Stock composition

plot_stockdist(fit, type = "stock_composition") # synonym: plot(fit, "stockcomp")

Suitability (fleet selection)

plot_suitability(fit) # synonym: plot(fit, "suitability")

Average length by age (growth)

plot_growth(fit) # synonym: plot(fit, "growth")

Age-length fit

Returns as many plots as there are separate age-length data sources. Only one plotted here to save space.

plot_agelength(fit, name = "EggaN_aldist_female") # synonym: plot(fit, "agelength")
#> $EggaN_aldist_female

Age composition

plot_agecomp(fit) # synonym: plot(fit, "agecomp"), also "stock.std" works

Residuals

plot_resid(fit) # synonym: plot(fit, "resid")

Likelihood

plot_likelihood(fit) # synonym: plot(fit, "likelihood")

plot_likelihood(fit, type = "weighted") # synonym: plot(fit, "weighted")

plot_likelihood(fit, type = "sums") # synonym: plot(fit, "sums")

Parameters

Parameter component weights:

plot_weight(fit) # synonym: plot(fit, "weight")

# plot_param(fit) # synonym: plot(fit, "param") # need to add bounds to g3_fit

Quickly plot central diagnostics

The gadget_plot() produces a range of diagnostic plots into a folder specified by the path argument. You may also use the file_type = "html" argument to save these plots into a single html file. There is also the make_html() to produce the html file directly without a wrapper function.

Found a bug or desire a feature?

The package is under an active development together with gadget3 framework. Please report bugs and write feature requests under Issues.