Package 'jjmR'

Title: Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model
Description: Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model.
Authors: Ricardo Oliveros-Ramos [cre, aut], Wencheng Lau-Medrano [aut], Giancarlo Moron [aut], Josymar Torrejon-Magallanes [aut], Niels Hintzen [aut], Enrique Ramos-Vasquez [ctb], Jim Ianelli [aut]
Maintainer: Ricardo Oliveros-Ramos <[email protected]>
License: GPL-2
Version: 1.2020.1
Built: 2026-10-11 10:41:45 UTC
Source: https://github.com/SPRFMO/jjmr

Help Index

Create a jjm.config object

Description

Construct a jjm.config object from data and control lists.

Usage

.getJjmConfig(data, control, ...)

Arguments

data

List of raw data elements for the JJM model.
control

List of control parameters, including modelName.
...

Unused.

Value

An object of class jjm.config.

Annex diagnostic plotting helpers

Description

Helpers for building benchmark annex diagnostic figures from JJM model outputs, including input metadata, composition fits, index diagnostics, retrospective plots, selectivity, stock status, stock-recruitment, Kobe plots, and historical retrospectives.

Usage

jjm_label(nm, stock_name = NULL)
jjm_pfa_palette(type = c("pfa", "fleet", "survey", "peel"))
extr_catch(mod, stock = 1)
extr_wtat_fsh(mod, stock = 1)
extr_wtat_srv(mod, stock = 1)
extr_agefits_fsh(mod, stock = 1)
extr_lenfits_fsh(mod, stock = 1)
extr_agefits_srv(mod, stock = 1)
extr_indices(mod, stock = 1)
extr_meanage_fsh(mod, stock = 1)
extr_meanage_srv(mod, stock = 1)
extr_meanlen_fsh(mod, stock = 1)
extr_effn(mod, stock = 1)
extr_catch_cv(mod, stock = 1)
extr_fished_unfished(mod, stock = 1)
extr_retro(retro, var = "SSB", stock = 1)
extr_q_breaks(mod)
extr_cv(mod, stock = 1)
extr_sel_fsh(mod, stock = 1)
extr_sel_srv(mod, stock = 1)
extr_sel_breaks(mod, type = c("fsh", "srv"))
extr_sr(mod, stock = 1)
extr_kobe(mod, stock = 1)
extr_francis(agefits, effn_df, grp_var = "fleet")
extr_q_trajectory(mod, stock = 1)
extr_survey_skill(mod, stock = 1)
has_comp(df, grp_var = NULL, grp_filter = NULL)
comp_fig_height(df, grp_var = NULL, grp_filter = NULL, ncol = 5,
  panel_h = 2.2, row2_h = 2.5, row3_h = 2.2)
facet_fig_height(n_panels, ncol = 2, panel_h = 3.5, min_h = 4)
plot_catch_fleet(mod, stock = 1, title = NULL)
calc_mohn_rho(df, n_peel = 5)
plot_retro(retro, var = "SSB", stock = 1, title = NULL)
plot_wtat(df, facet_var, title = NULL, years = NULL)
plot_wtat_cohort(df, facet_var, title = NULL, years = NULL)
plot_comp_fits(df, x_var, grp_var, grp_filter = NULL, x_lab = "Age",
  title = NULL)
plot_indices_v2(mod, stock = 1, title = NULL)
plot_comp_ridge(df, x_var = "age", facet_var = "fleet", x_lab = "Age",
  title = NULL)
plot_sel_ridge(df, facet_var, title = NULL, breaks_df = NULL)
plot_fit_diagnostics(df, title = NULL)
plot_effn(mod, stock = 1, title = NULL)
plot_meanstat(df, facet_var, y_lab = "Mean age (years)", title = NULL)
plot_fished_unfished(mod, stock = 1, title = NULL)
plot_summary_sheet(mod, stock = 1, title = NULL)
plot_sr(mod, stock = 1, title = NULL)
plot_kobe(mod, stock = 1, title = NULL)
strong_cohorts(mod, stock = 1, n = 3)
annotate_cohorts(years, colour = PFA_GREEN, label_size = 3)
plot_francis(mod, stock = 1, title = NULL)
plot_q_trajectory(mod, stock = 1, title = NULL)
plot_survey_skill(mod, stock = 1, title = NULL)
plot_metadata_overview(mod, title = NULL)
read_historic_retro(file,
  exclude_assessment_types = c("benchmark", "mod1.4"))
plot_historic_retro(data, quantity = c("stock", "reference"),
  title = NULL)

Arguments

mod

A jjm.output object returned by readJJM.
stock

Stock index.
retro

A retrospective object loaded from a JJM retrospective RData file.
df, agefits, effn_df, data

Data frames or tibbles returned by the corresponding extractor functions.
title

Optional plot title.
var

Retrospective variable, such as "SSB", "R", or "F".
type, quantity

Character option selecting a palette, selectivity type, or historical retrospective plot group.
grp_var

Grouping variable name.
grp_filter

Optional group value to filter.
ncol

Number of panels per row.
panel_h

Height per panel row.
row2_h

Height for the bubble residual row.
row3_h

Height for the marginal residual row.
n_panels

Number of panels.
min_h

Minimum figure height.
n_peel

Number of retrospective peels to include.
facet_var

Facet variable name.
x_var

X variable name.
x_lab

X-axis label.
breaks_df

Optional selectivity break-year data.
y_lab

Y-axis label.
n

Number of cohort years to return.
colour

Annotation colour.
label_size

Annotation label size.
exclude_assessment_types

Assessment types to remove before plotting historical retrospectives.
nm, stock_name

Model name and optional stock label used to construct a display label.
file

Path to a historical retrospective CSV file.
years

Years to annotate or plot.

Value

Extractor functions return tibbles or lists. Plot functions return ggplot2 or patchwork objects.

Examples

## Not run: 
mod <- readJJM("h1_1.14", path = "assessment/config",
  input = "assessment/input", output = "assessment/results")

plot_metadata_overview(mod)
plot_catch_fleet(mod, title = jjm_label("h1_1.14"))
plot_indices_v2(mod)

## End(Not run)

Annotate strong cohort years on a ggplot

Description

Annotate strong cohort years on a ggplot

Usage

annotate_cohorts(years, colour = PFA_GREEN, label_size = 3)

Arguments

years

Cohort years.
colour

Annotation colour.
label_size

Text size.

Value

A list of ggplot layers.

Calculate Mohn's rho

Description

Calculate Mohn's rho

Usage

calc_mohn_rho(df, n_peel = 5)

Arguments

df

Retrospective tibble from [extr_retro()].
n_peel

Number of peels to include.

Value

Numeric Mohn's rho.

Change the internal name of a model

Description

This function internally replaces the name of a JJM output object with a user-specified string. Mostly useful for plots.

Usage

changeNameModel(modList, nameVector)

Arguments

modList

A list of JJM model output objects.
nameVector

Character vector of replacement model names.

Examples

## Not run: 
recmods <- compareModels(c("mod1.00.hl","mod1.00.ll","mod1.00.hs","mod1.00.ls"))

changeNameModel(recmods,c( "h=0.8, full series","h=0.8, short series","h=0.65, full series","h=0.65, short series" ))

## End(Not run)

Coerce a vector to character or numeric

Description

Coerce a vector to character or numeric

Usage

coerce(x, to = c("chr", "num", "num_chr"))

Arguments

x

Vector to coerce
to

One of "chr", "num", "num_chr"

Combine outputs

Description

This function takes model objects (class outputs) of JJM and generate an object with combined models.

Usage

combineModels(...)

Arguments

...

One or more output objects, to be combined to list of models.

Examples

## Not run: 
mod1 <- runJJM(modelName = "mod2.1")
mod2 <- runJJM(modelName = "mod2.2")
mod3 <- runJJM(modelName = "mod2.3")

mod_123 = combineModels(mod1, mod2, mod3)

## End(Not run)

Calculate figure height for composition fits

Description

Calculate figure height for composition fits

Usage

comp_fig_height(
  df,
  grp_var = NULL,
  grp_filter = NULL,
  ncol = 5,
  panel_h = 2.2,
  row2_h = 2.5,
  row3_h = 2.2
)

Arguments

df

Composition fit tibble.
grp_var

Optional grouping variable name.
grp_filter

Optional group value to filter.
ncol

Number of panels per row.
panel_h

Height per row of year panels.
row2_h

Height for the bubble residual row.
row3_h

Height for the marginal residual row.

Value

Numeric figure height.

Compare combined JJM outputs

Description

This function takes a vector of model names, reads in the JJM runs, and combines them. Basically a wrapper function for combineModels. Assumes model runs are in the same folder.

Usage

compareModels(mods)

Arguments

mods

Character vector of model names to compare.

Examples

## Not run: 

mod_123 = compareModels(c("h1_0.00", "h1_0.01", "h1_0.02")

## End(Not run)

Generate Assessment plots from single model

Description

Function to generate plots from results of readJJM function

Usage

diagnostics(object, ...)

Arguments

object

Object ob class outputs.
...

Extra arguments

Examples

## Not run: 
model = readJJM(modelName = "mod2.4")
diagnostics(object = model)

## End(Not run)

Extract fishery age-composition fits

Description

Extract fishery age-composition fits

Usage

extr_agefits_fsh(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with observed and predicted fishery age compositions.

Extract survey age-composition fits

Description

Extract survey age-composition fits

Usage

extr_agefits_srv(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with observed and predicted survey age compositions.

Extract observed catch by fleet

Description

Extract observed catch by fleet

Usage

extr_catch(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with 'year', 'catch', and 'fleet'.

Extract catch observation CVs

Description

Extract catch observation CVs

Usage

extr_catch_cv(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with catch CVs by fleet and year.

Extract index CVs

Description

Extract index CVs

Usage

extr_cv(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with survey index CVs.

Extract input composition sample sizes

Description

Extract input composition sample sizes

Usage

extr_effn(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with composition input sample sizes.

Extract fished and unfished total biomass

Description

Extract fished and unfished total biomass

Usage

extr_fished_unfished(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with total biomass by scenario.

Calculate Francis T1.8 effective sample sizes

Description

Calculate Francis T1.8 effective sample sizes

Usage

extr_francis(agefits, effn_df, grp_var = "fleet")

Arguments

agefits

Age-composition fit data.
effn_df

Input sample-size data from [extr_effn()].
grp_var

Group variable, '"fleet"' or '"survey"'.

Value

A tibble with input and Francis effective sample sizes.

Extract standardised survey index fits

Description

Extract standardised survey index fits

Usage

extr_indices(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with standardised observed and modelled index values.

Extract Kobe phase-plot data

Description

Extract Kobe phase-plot data

Usage

extr_kobe(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with 'year', 'bbmsy', and 'ffmsy'.

Extract fishery length-composition fits

Description

Extract fishery length-composition fits

Usage

extr_lenfits_fsh(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with observed and predicted fishery length compositions.

Extract fishery mean age fits

Description

Extract fishery mean age fits

Usage

extr_meanage_fsh(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with fishery mean-age observations and fits.

Extract survey mean age fits

Description

Extract survey mean age fits

Usage

extr_meanage_srv(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with survey mean-age observations and fits.

Extract fishery mean length fits

Description

Extract fishery mean length fits

Usage

extr_meanlen_fsh(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with fishery mean-length observations and fits.

Extract q break years

Description

Extract q break years

Usage

extr_q_breaks(mod)

Arguments

mod

A 'jjm.output' object from [readJJM()].

Value

A tibble with survey names and q break years.

Extract q trajectories

Description

Extract q trajectories

Usage

extr_q_trajectory(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with catchability by survey and year.

Extract retrospective data

Description

Extract retrospective data

Usage

extr_retro(retro, var = "SSB", stock = 1)

Arguments

retro

A retrospective object loaded from a JJM retrospective RData file.
var

Variable to extract. '"SSB"' and '"R"' use direct retrospective entries. '"F"' averages the first column of all 'F_fsh_*' entries.
stock

Stock index.

Value

A tibble with 'year', 'est', optional confidence limits, and 'peel'.

Extract selectivity block break years

Description

Extract selectivity block break years

Usage

extr_sel_breaks(mod, type = c("fsh", "srv"))

Arguments

mod

A 'jjm.output' object from [readJJM()].
type

'"fsh"' for fisheries or '"srv"' for surveys.

Value

A tibble of break years.

Extract fishery selectivity-at-age

Description

Extract fishery selectivity-at-age

Usage

extr_sel_fsh(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with fishery selectivity-at-age.

Extract survey selectivity-at-age

Description

Extract survey selectivity-at-age

Usage

extr_sel_srv(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with survey selectivity-at-age.

Extract stock-recruitment pairs and curve

Description

Extract stock-recruitment pairs and curve

Usage

extr_sr(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A list with 'pairs', 'curve', and 'steepness'.

Extract survey skill data

Description

Extract survey skill data

Usage

extr_survey_skill(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with survey log-ratios and model SSB direction.

Extract fishery weight-at-age data

Description

Extract fishery weight-at-age data

Usage

extr_wtat_fsh(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with 'year', 'fleet', 'age', and 'weight'.

Extract survey weight-at-age data

Description

Extract survey weight-at-age data

Usage

extr_wtat_srv(mod, stock = 1)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.

Value

A tibble with 'year', 'survey', 'age', and 'weight'.

Calculate figure height for faceted plots

Description

Calculate figure height for faceted plots

Usage

facet_fig_height(n_panels, ncol = 2, panel_h = 3.5, min_h = 4)

Arguments

n_panels

Number of panels.
ncol

Number of panels per row.
panel_h

Height per panel row.
min_h

Minimum height.

Value

Numeric figure height.

Calculate or input a fixed Bmsy value for the jjm model Updates the msy_mt table in the jjm output with new B/Bmsy ratios.

Description

Calculate or input a fixed Bmsy value for the jjm model Updates the msy_mt table in the jjm output with new B/Bmsy ratios.

Usage

fixed_bmsy(mod, bmsy_in = NULL, dyn = FALSE)

Arguments

mod

jjm object that is a list of lists
bmsy_in

A number (or vector of numbers if multiple stocks) to input as Bmsy. If not filled, calculated as the average of the Bmsy estimated for the last ten years (as determined in SCW14 benchmark 2022)
dyn

Logical value to indicate whether a dynamic Bmsy should be calculated

Value

A model

Examples

# fixed_bmsy(mod_h1_1.00, bmsy_in=5500) # To input a fixed Bmsy
# fixed_bmsy(mod_h1_1.00) # To calculate the Bmsy

Get fits to indices

Description

Get fits to indices

Usage

get_age_fits(models)

Arguments

models

an object of class jjm.output

Value

a tidy dataframe of age fits

Get estimated catchability coefficients

Description

Get estimated catchability coefficients

Usage

get_catchabilities(models)

Arguments

models

an object of class jjm.output

Value

a data frame of estimated catchabilities

Get fishing mortality at age

Description

Get fishing mortality at age

Usage

get_fishing_mortality(models)

Arguments

models

an object of class jjm.output

Value

a tidy dataframe of fishing mortality at age

Get fits to indices

Description

Get fits to indices

Usage

get_index_fits(models)

Arguments

models

an object of class jjm.output

Value

a tidy dataframe of index fits

Get fits to length compositions

Description

Get fits to length compositions

Usage

get_len_fits(models)

Arguments

models

an object of class jjm.output

Value

a tidy dataframe of length composition fits

Get and tidy msy_my table

Description

Get and tidy msy_my table

Usage

get_msy_mt(models)

Arguments

models

series of class jjm.output

Value

a tidy msy_mt

Examples

## Not run: 

mod0.00 <- readJJM("h2_0.00", path = "config", input = "input")
get_msy_mt(mod0.00)

## End(Not run)

Get estimated recruits

Description

Get estimated recruits

Usage

get_recruits(models)

Arguments

models

an object of class jjm.output

Value

a tidy dataframe of recruits

Get and tidy selectivity-at-age ogives over time by model and fleet

Description

Get and tidy selectivity-at-age ogives over time by model and fleet

Usage

get_selectivities(models)

Arguments

models

an object of class jjm.output

Value

a tidy data frame of selectivity estimates

Examples

## Not run: 
h1.mod <- jjmR::readJJM("h2_0.02", path = "config", input = "input")
selectivities <- get_selectivities(h1.mod)

## End(Not run)

Get total metrics (biomass, spawning biomass, and recruitment)

Description

Get total metrics (biomass, spawning biomass, and recruitment)

Usage

get_totals(models)

Arguments

models

an object of class jjm.output

Value

a dataframe of total values

Add hypothesis number to a model name

Description

Add hypothesis number to a model name

Usage

geth(mod, h = hyp)

Arguments

mod

A character string of a model name.
h

A character string containing the hypothesis to use.

Value

A character string containing the hypothesis name and the model name.

Examples

geth("1.00", "h1")

Get elements of a list by string matching on name

Description

Get elements of a list by string matching on name

Usage

getter(x, pattern = "^sel_", things = NA)

Arguments

x

the object
pattern

the string pattern (regex supported) to search for
things

Optional preselected object list; defaults to NA.

Value

an object subset to matches in names with strings

Compute a gray color ramp

Description

Compute a gray color ramp

Usage

gray_ramp(n)

Arguments

n

Number of shades

Value

Character vector of hex grays

Check whether composition data are available

Description

Check whether composition data are available

Usage

has_comp(df, grp_var = NULL, grp_filter = NULL)

Arguments

df

Composition fit tibble.
grp_var

Optional grouping variable name.
grp_filter

Optional group value to filter.

Value

'TRUE' when observed composition rows exist.

Build a publication label from a JJM model name

Description

Build a publication label from a JJM model name

Usage

jjm_label(nm, stock_name = NULL)

Arguments

nm

Model name, such as '"h1_1.14"' or '"h2_1.14"'.
stock_name

Optional stock label to append.

Value

A character label.

JJM annex diagnostic palettes

Description

JJM annex diagnostic palettes

Usage

jjm_pfa_palette(type = c("pfa", "fleet", "survey", "peel"))

Arguments

type

Palette to return: '"pfa"', '"fleet"', '"survey"', or '"peel"'.

Value

A named character vector of hex colours.

Kobe plot

Description

This function create a kobe plot from JJM model outputs

Usage

kobe(
  obj,
  add = FALSE,
  col = "black",
  stock = 1,
  Bref = 1,
  Fref = 1,
  Blim = Bref,
  Flim = Fref,
  xlim = NULL,
  ylim = NULL,
  engine = "ggplot",
  ...
)

Arguments

obj

a jjm model outputs object.
add

boolean, add to an existing kobe plot?
col

color for the lines and points.
stock

Number of the stock chosen for the kobe plot.
Bref

Reference point for B/B_MSY, default=1.
Fref

Reference point for F/F_MSY, default=1.
Blim

Limit reference point for B/B_MSY, default=0.5.
Flim

Limit reference point for F/F_MSY, default=1.5.
xlim

'x' axis limits.
ylim

'y' axis limits.
engine

Plotting engine, either "ggplot" or "lattice".
...

Additional parameters passed to plot.

Examples

## Not run: 
kobe(model)

## End(Not run)

Melt an age-or-length matrix into a long tibble

Description

Melt an age-or-length matrix into a long tibble

Usage

melt_matrix(mat, years = NULL, ages = NULL, class = "age")

Arguments

mat

A matrix with years in column 1 and data in subsequent columns
years

Vector of years (if not the first column)
ages

Ages or lengths
class

Name of the grouping variable (e.g. "age" or "length")

Value

A tibble with columns 'year', 'value', and '<class>'

Bar+line plot of observed vs predicted catch-at-age

Description

Bar+line plot of observed vs predicted catch-at-age

Usage

plot_catch_age_fits(out, ages, fleets = NULL)

Arguments

out

jjm.out list from runJJM()
ages

integer vector of ages
fleets

optional character vector; default = all fleets

Bubble plot of catch-at-age residuals

Description

Bubble plot of catch-at-age residuals

Usage

plot_catch_age_residuals(out, ages, fleets = NULL)

Arguments

out

jjm.out list from runJJM()
ages

integer vector of ages
fleets

optional character vector; default = all fleets

Plot catch by fleet

Description

Plot catch by fleet

Usage

plot_catch_fleet(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A ggplot or patchwork object.

Plot composition fits and residuals

Description

Plot composition fits and residuals

Usage

plot_comp_fits(
  df,
  x_var,
  grp_var,
  grp_filter = NULL,
  x_lab = "Age",
  title = NULL
)

Arguments

df

Composition fit data from an 'extr_*fits_*()' function.
x_var

X variable, usually '"age"' or '"length_bin"'.
grp_var

Grouping variable, usually '"fleet"' or '"survey"'.
grp_filter

Optional group value.
x_lab

X-axis label.
title

Optional plot title.

Value

A patchwork object.

Plot observed composition ridges

Description

Plot observed composition ridges

Usage

plot_comp_ridge(
  df,
  x_var = "age",
  facet_var = "fleet",
  x_lab = "Age",
  title = NULL
)

Arguments

df

Composition fit data.
x_var

X variable, usually '"age"' or '"length_bin"'.
facet_var

Facet variable, usually '"fleet"' or '"survey"'.
x_lab

X-axis label.
title

Optional plot title.

Value

A ggplot object.

Plot input composition sample sizes

Description

Plot input composition sample sizes

Usage

plot_effn(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A ggplot object.

Plot fished and unfished biomass

Description

Plot fished and unfished biomass

Usage

plot_fished_unfished(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A ggplot object.

Plot weight at age in the fishery

Description

Plot weight at age in the fishery

Usage

plot_fishery_weight(out, ages)

Arguments

out

A jjm output list
ages

Vector of ages

Plot standard index fit diagnostics

Description

Plot standard index fit diagnostics

Usage

plot_fit_diagnostics(df, title = NULL)

Arguments

df

Index fit data, usually one survey from [extr_indices()].
title

Optional plot title.

Value

A patchwork object.

Plot Francis T1.8 reweighting diagnostics

Description

Plot Francis T1.8 reweighting diagnostics

Usage

plot_francis(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A ggplot object.

Plot historical retrospective diagnostics

Description

Plot historical retrospective diagnostics

Usage

plot_historic_retro(data, quantity = c("stock", "reference"), title = NULL)

Arguments

data

A prepared data frame from [read_historic_retro()] or a CSV file path.
quantity

Plot group: '"stock"' for SSB/F/recruitment or '"reference"' for reference points.
title

Optional patchwork title.

Value

A patchwork object.

Plot index fits with input CVs

Description

Plot index fits with input CVs

Usage

plot_indices_v2(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A ggplot or patchwork object.

Plot Kobe phase plot

Description

Plot Kobe phase plot

Usage

plot_kobe(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A ggplot object.

Plot mean age or mean length fits

Description

Plot mean age or mean length fits

Usage

plot_meanstat(df, facet_var, y_lab = "Mean age (years)", title = NULL)

Arguments

df

Data from 'extr_mean*()' functions.
facet_var

Facet variable.
y_lab

Y-axis label.
title

Optional plot title.

Value

A ggplot object.

Plot metadata overview

Description

Plot metadata overview

Usage

plot_metadata_overview(mod, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
title

Optional plot title.

Value

A ggplot object showing index, age-composition, and length-composition years by data source.

Plot q trajectories

Description

Plot q trajectories

Usage

plot_q_trajectory(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A ggplot object.

Plot retrospective peels

Description

Plot retrospective peels

Usage

plot_retro(retro, var = "SSB", stock = 1, title = NULL)

Arguments

retro

A retrospective object loaded from a JJM retrospective RData file.
var

Variable to extract. '"SSB"' and '"R"' use direct retrospective entries. '"F"' averages the first column of all 'F_fsh_*' entries.
stock

Stock index.
title

Optional plot title.

Value

A ggplot object.

Plot selectivity ridges

Description

Plot selectivity ridges

Usage

plot_sel_ridge(df, facet_var, title = NULL, breaks_df = NULL)

Arguments

df

Selectivity data from [extr_sel_fsh()] or [extr_sel_srv()].
facet_var

Facet variable.
title

Optional plot title.
breaks_df

Optional break-year data from [extr_sel_breaks()].

Value

A ggplot object.

Plot selectivities by age, year, fleet, and model

Description

Plot selectivities by age, year, fleet, and model

Usage

plot_selectivities(
  sels,
  fleet = "fsh",
  alpha = 0.4,
  scale = 4,
  size = 0.5,
  years = "all"
)

Arguments

sels

selectivity data frame generated by get_selectivities
fleet

fleets to plot: "fsh" (fishery), "ind" (survey), or "all" (both)
alpha

Line opacity.
scale

Scaling factor for the panel strip color gradient.
size

Line width.
years

Years to plot, or "all" for every year.

Value

a ggplot2 plot object

Examples

## Not run: 

oldnewMods <- combineModels(mod0.00,mod_prev)
selectivities <- get_selectivities(oldnewMods)
plot_selectivities(selectivities)


## End(Not run)

Plot stock-recruitment relationship

Description

Plot stock-recruitment relationship

Usage

plot_sr(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A ggplot object.

Plot a summary diagnostics sheet

Description

Plot a summary diagnostics sheet

Usage

plot_summary_sheet(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A patchwork object.

Plot survey skill ROC curves

Description

Plot survey skill ROC curves

Usage

plot_survey_skill(mod, stock = 1, title = NULL)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
title

Optional plot title.

Value

A ggplot object.

Plot weight-at-age over time

Description

Plot weight-at-age over time

Usage

plot_wtat(df, facet_var, title = NULL, years = NULL)

Arguments

df

Data from [extr_wtat_fsh()] or [extr_wtat_srv()].
facet_var

Facet variable, usually '"fleet"' or '"survey"'.
title

Optional plot title.
years

Optional vector of years to plot.

Value

A ggplot object.

Plot weight-at-age by cohort

Description

Plot weight-at-age by cohort

Usage

plot_wtat_cohort(df, facet_var, title = NULL, years = NULL)

Arguments

df

Data from [extr_wtat_fsh()] or [extr_wtat_srv()].
facet_var

Facet variable, usually '"fleet"' or '"survey"'.
title

Optional plot title.
years

Optional vector of years to plot.

Value

A ggplot object.

Plot method for jjm.diag objects

Description

Creates diagnostic plots from the JJM model diagnostics based on specified parameters. Can generate plots for model inputs (data) or outputs across different models and stocks.

Usage

## S3 method for class 'jjm.diag'
plot(
  x,
  what = c("data", "output"),
  model = NULL,
  stock = NULL,
  var = NULL,
  fleet = NULL,
  plot = TRUE,
  ...
)

Arguments

x

An object of class 'jjm.diag'
what

Character vector specifying which type of diagnostics to plot. Options are "data" (or deprecated "input") and "output". Default is c("data", "output").
model

Character vector of model names to include. If NULL (default), all models are used.
stock

Character vector of stock names to include. If NULL (default), all stocks are used.
var

Character vector of variable names to include. If NULL (default), all variables are used.
fleet

Character vector or numeric vector of fleet indices to include. If NULL (default), all fleets are used.
plot

Logical. If TRUE (default), plots are displayed. If FALSE, plot objects are returned.
...

Additional arguments passed to internal plotting functions

Value

If plot=TRUE, returns invisibly. If plot=FALSE, returns a list of plot objects.

Examples

## Not run: 
diagnostics <- diag.jjm("path/to/model")
# Plot all diagnostics
plot(diagnostics)

# Plot only data diagnostics for a specific model and stock
plot(diagnostics, what = "data", model = "Model1", stock = "Stock1")

# Return plot objects without displaying
plot_objects <- plot(diagnostics, plot = FALSE)

## End(Not run)

Plot diagnostics

Description

Plot diagnostics

Usage

## S3 method for class 'jjm.diagnostics'
plot(x, which = names(x), ...)

Arguments

x

A summary.jjm.diagnostics
which

Vector of named diagnostics to render
...

Additional arguments. Currently ignored.

Plot method for jjm.output objects

Description

Creates various plots from the JJM model output based on the specified type.

Usage

## S3 method for class 'jjm.output'
plot(
  x,
  what = "biomass",
  stack = TRUE,
  endvalue = FALSE,
  total = FALSE,
  combine = FALSE,
  cols = NULL,
  poslegend = "right",
  scen = 1,
  ...
)

Arguments

x

An object of class 'jjm.output'
what

Character string specifying the type of plot. Options include:

  • "biomass" - Plot biomass over time

  • "recruitment" - Plot recruitment over time

  • "ssb" - Plot spawning stock biomass over time

  • "noFishTB" - Plot unfished total biomass

  • "ftot" - Plot total fishing mortality

  • "kobe" - Create a Kobe plot

  • "catchProj" - Plot catch projections

  • "ssbProj" - Plot SSB projections

  • "totalProj" - Plot total projections

  • "catchProjScen" - Plot catch projection scenarios

  • "ssbProjScen" - Plot SSB projection scenarios

  • "ratioSSB_F" - Plot ratio of SSB to F

  • "ratioSSB" - Plot ratio of SSB

  • "selectivity" - Plot selectivity curves

stack

Logical. If TRUE, stack multiple series in one plot. Default is TRUE.
endvalue

Logical. If TRUE, display end values on plot. Default is FALSE.
total

Logical. If TRUE, include total values. Default is FALSE.
combine

Logical. If TRUE, combine multiple plots. Default is FALSE.
cols

Optional vector of colors for plotting
poslegend

Position of the legend. Default is "right".
scen

Integer. Scenario number for projection plots. Default is 1.
...

Additional arguments passed to plotting functions

Value

A plot object (typically a grid or ggplot object)

Examples

## Not run: 
model <- read.jjm("path/to/model")
plot(model, what = "biomass")
plot(model, what = "ssb", stack = FALSE)
plot(model, what = "kobe")

## End(Not run)

Print a jjm.config object

Description

Print a jjm.config object

Usage

## S3 method for class 'jjm.config'
print(x, ...)

Arguments

x

A jjm.config object.
...

Additional arguments (ignored).

Value

Invisibly returns x.

Print method for jjm.diag objects

Description

Prints a summary of the JJM diagnostic object, displaying information about available input and output plots for each model and stock.

Usage

## S3 method for class 'jjm.diag'
print(x, ...)

Arguments

x

An object of class 'jjm.diag'
...

Additional arguments passed to print methods

Value

Invisibly returns the input object (for use in pipelines)

Examples

## Not run: 
diagnostics <- diag.jjm("path/to/model")
print(diagnostics)

## End(Not run)

Print method for jjm.output objects

Description

Prints a summary of the JJM model output object, displaying basic information about the model, stocks, and data sources.

Usage

## S3 method for class 'jjm.output'
print(x, ...)

Arguments

x

An object of class 'jjm.output'
...

Additional arguments passed to print methods

Value

Invisibly returns the input object (for use in pipelines)

Examples

## Not run: 
model <- read.jjm("path/to/model")
print(model)

## End(Not run)

Print a summary of jjm.config

Description

Print a summary of jjm.config

Usage

## S3 method for class 'summary.jjm.config'
print(x, ...)

Arguments

x

A summary.jjm.config object.
...

Additional arguments (ignored).

Value

Invisibly returns x.

Print method for summary.jjm.diag objects

Description

Prints the detailed diagnostics information from a summary.jjm.diag object, showing both input and output plot details.

Usage

## S3 method for class 'summary.jjm.diag'
print(x, ...)

Arguments

x

An object of class 'summary.jjm.diag'
...

Additional arguments passed to print methods

Value

Invisibly returns the input object (for use in pipelines)

Print method for summary.jjm.output objects

Description

Prints the tables and plots generated by the summary method for jjm.output objects.

Usage

## S3 method for class 'summary.jjm.output'
print(x, ...)

Arguments

x

An object of class 'summary.jjm.output'
...

Additional arguments passed to print methods

Value

Invisibly returns the input object (for use in pipelines)

Read historical retrospective CSV data

Description

Read historical retrospective CSV data

Usage

read_historic_retro(file, exclude_assessment_types = c("benchmark", "mod1.4"))

Arguments

file

CSV file path.
exclude_assessment_types

Assessment types to remove before plotting.

Value

A prepared data frame.

Read external files

Description

Read external files

Usage

readExFiles(
  fileName,
  type,
  path = NULL,
  version = "2015MS",
  parameters = FALSE,
  parData,
  nameFishery,
  nameIndex,
  nAges,
  nStock = NULL
)

Arguments

fileName

filename
type

type
path

path
version

version of JJM, default to "2015MS" (2015 SC multi-stock).
parameters

parameters
parData

parData
nameFishery

nameFishery
nameIndex

nameIndex
nAges

nAges
nStock

nStock

Read a model or list of models

Description

Function to read models and list if models and generate results

Usage

readJJM(
  model,
  path = NULL,
  output = "results",
  input = NULL,
  version = "2015MS",
  ...
)

Arguments

model

String with the name of model that will be readed or run.
path

Directory where the 'admb' folder is located.
output

Path to the model outputs directory.
input

Path to model inputs directory.
version

version of JJM, default to "2015MS" (2015 SC multi-stock).
...

Extra arguments

Examples

## Not run: 
readJJM(model = "mod2.4")

## End(Not run)

Read dat and ctl files from disk to create a jjm.config object.

Description

Store in an R object (of class jjm.config) the dat and ctl files needed to run a model.

Usage

readJJMConfig(model, path, input = NULL, ...)

Arguments

model

Model object or outputs
path

Path to the ctl file
input

Path to the input files
...

Additional arguments passed to other functions.

Examples

## Not run: 
readJJMConfig(mod1)

## End(Not run)

Create a report from JJM outputs

Description

Function to create and save reports in PDF and MS Word formats.

Usage

report(object, format, output, tangle = FALSE, tidy = TRUE, ...)

Arguments

object

The object to create the report with, can be of classes 'jjm.output' or 'jjm.diag' as created with readJJM or diagnostics.
format

Format for the report: either "pdf", "html" or "word".
output

Path to save the report, by default the working directory.
tangle

Boolean, if TRUE the R script to create the report is produced.
tidy

Boolean, if TRUE the intermediate files (Rmd, tex) are deleted.
...

Extra arguments

Examples

## Not run: 
report(mod0.0)

## End(Not run)

Run a retrospective analysis diagnostic for a JJM model

Description

Run a retrospective analysis for a model

Usage

retro(
  model,
  n = 5,
  output = "results",
  exec = NULL,
  parallel = FALSE,
  temp = NULL,
  wait = TRUE,
  iprint = 100,
  ...
)

Arguments

model

An object of class jjm.output
n

Number of years to run a retrospective analysis.
output

Path to save results.
exec

Path to JJM executable file.
parallel

Boolean flag to run models in parallel.
temp

Folder to run retrospective analysis. If NULL, a temporal folder is used.
wait

Boolean, passed to runJJM, should we wait for the parameter estimation?
iprint

Command line argument passed to jjm.
...

Additional arguments passed to other functions.

Examples

## Not run: 
retro(mod1)

## End(Not run)

Fit, run, read and plot a JJM model

Description

Shortcut to fit, run, read and plot a JJM model

Usage

runit(
  mod,
  est = FALSE,
  exec = NULL,
  path = "config",
  input = "input",
  output = "results",
  version = "2015MS",
  pdf = FALSE,
  portrait = TRUE,
  ...
)

Arguments

mod

A character specifying the name of a model (by it's ctl filename).
est

Boolean, should we run the parameter estimation for a model?
exec

Path to the JJM executable file. By default, 'jjms' will be used.
path

Directory where the configuration files will be written.
input

Input
output

Folder to save the outputs, 'arc' by default.
version

version of JJM, default to "2015MS" (2015 SC multi-stock).
pdf

Produce outputs in a pdf file?
portrait

Orientation of the pdf output, default TRUE.
...

Additional arguments passed to runJJM.

Examples

## Not run: 
writeJJM(mod1)

## End(Not run)

Run a JJM model

Description

Function to run one or several JJM models

Usage

runJJM(
  models,
  path = NULL,
  output = "results",
  input = NULL,
  exec = NULL,
  version = NULL,
  useGuess = FALSE,
  guess = NULL,
  piner = NULL,
  iprint = 100,
  wait = TRUE,
  parallel = FALSE,
  temp = NULL,
  ...
)

Arguments

models

String with the name of the models to be run.
path

Directory where the 'admb' folder is located.
output

Folder to save the outputs, 'arc' by default.
input

Input
exec

Path to the jjm executable
version

version of JJM, default to "2015MS" (2015 SC multi-stock).
useGuess

boolean, to use an initial guess for the parameters?
guess

File with the initial guess for the parameters. If NULL, will use model.par in the output folder.
piner

A number to start the profiling on the meanlogrec
iprint

iprint parameter for the JJM model, 100 by default.
wait

boolean, wait for the model to finish? Forced to be TRUE.
parallel

Should model run in parallel? A cluster need to be setup to be used with foreach.
temp

character, path for a temporal directory to run models, if NULL a temporal folder is automaticaly created.
...

Arguments passed from system function.

Examples

## Not run: 
model = runJJM(models = "mod2.4")

## End(Not run)

Run JJM models (default method)

Description

Executes one or more JJM model runs, optionally in parallel.

Usage

## Default S3 method:
runJJM(
  models,
  path = NULL,
  output = "results",
  input = NULL,
  exec = NULL,
  version = NULL,
  useGuess = FALSE,
  guess = NULL,
  piner = NULL,
  iprint = 100,
  wait = TRUE,
  parallel = FALSE,
  temp = NULL,
  ...
)

Arguments

models

Character vector of model filenames.
path

Optional directory containing model files.
output

Directory for model results (created if missing).
input

Directory for input files (default = model directory).
exec

Path to JJM executable.
version

Executable version (ignored if exec provided).
useGuess

Logical; whether to use starting parameter guesses.
guess

Vector of guess filenames or logical.
piner

Additional runner parameters.
iprint

Printing control for JJM output.
wait

Logical; whether to wait for completion before returning.
parallel

Logical; whether to run models in parallel.
temp

Directory for temporary files (default = tempdir()).
...

Additional arguments passed to internal runner.

Value

Invisibly returns the path to temp used for input files.

Run JJM models for jjm.config

Description

Run JJM models for jjm.config

Usage

## S3 method for class 'jjm.config'
runJJM(
  models,
  path = NULL,
  output = "results",
  input = NULL,
  exec = NULL,
  version = NULL,
  useGuess = FALSE,
  guess = NULL,
  piner = NULL,
  iprint = 100,
  wait = TRUE,
  parallel = FALSE,
  temp = NULL,
  ...
)

Arguments

models

Character vector of model filenames.
path

Optional directory containing model files.
output

Directory for model results (created if missing).
input

Directory for input files (default = model directory).
exec

Path to JJM executable.
version

Executable version (ignored if exec provided).
useGuess

Logical; whether to use starting parameter guesses.
guess

Vector of guess filenames or logical.
piner

Additional runner parameters.
iprint

Printing control for JJM output.
wait

Logical; whether to wait for completion before returning.
parallel

Logical; whether to run models in parallel.
temp

Directory for temporary files (default = tempdir()).
...

Additional arguments passed to internal runner.

Run JJM models for jjm.output

Description

Run JJM models for jjm.output

Usage

## S3 method for class 'jjm.output'
runJJM(
  models,
  path = NULL,
  output = "results",
  input = NULL,
  exec = NULL,
  version = NULL,
  useGuess = FALSE,
  guess = NULL,
  piner = NULL,
  iprint = 100,
  wait = TRUE,
  parallel = FALSE,
  temp = NULL,
  ...
)

Arguments

models

Character vector of model filenames.
path

Optional directory containing model files.
output

Directory for model results (created if missing).
input

Directory for input files (default = model directory).
exec

Path to JJM executable.
version

Executable version (ignored if exec provided).
useGuess

Logical; whether to use starting parameter guesses.
guess

Vector of guess filenames or logical.
piner

Additional runner parameters.
iprint

Printing control for JJM output.
wait

Logical; whether to wait for completion before returning.
parallel

Logical; whether to run models in parallel.
temp

Directory for temporary files (default = tempdir()).
...

Additional arguments passed to internal runner.

Identify strong cohorts

Description

Identify strong cohorts

Usage

strong_cohorts(mod, stock = 1, n = 3)

Arguments

mod

A 'jjm.output' object from [readJJM()].
stock

Stock index.
n

Number of recruitment years to return.

Value

Integer vector of cohort years.

Summarize a jjm.config object

Description

Summarize a jjm.config object

Usage

## S3 method for class 'jjm.config'
summary(object, ...)

Arguments

object

A jjm.config object.
...

Additional arguments (ignored).

Value

An object of class summary.jjm.config containing model names.

Summary method for jjm.diag objects

Description

Creates a detailed summary of JJM diagnostics, including information about input and output plots for model evaluation.

Usage

## S3 method for class 'jjm.diag'
summary(object, ...)

Arguments

object

An object of class 'jjm.diag'
...

Additional arguments passed to internal functions

Value

An object of class 'summary.jjm.diag' containing detailed diagnostics

Examples

## Not run: 
diagnostics <- diag.jjm("path/to/model")
diag_summary <- summary(diagnostics)
print(diag_summary)

## End(Not run)

Summarize all diagnostics from a jjm run

Description

Summarize all diagnostics from a jjm run

Usage

## S3 method for class 'jjm.diagnostics'
summary(object, ...)

Arguments

object

A list returned by runJJM
...

Additional arguments. Currently ignored.

Summary method for jjm.output objects

Description

Generates a detailed summary of the JJM model output, including parameter tables, likelihood tables, projection tables (if requested), and summary plots.

Usage

## S3 method for class 'jjm.output'
summary(
  object,
  Projections = FALSE,
  Fmult = NULL,
  BiomProj = NULL,
  CapProj = NULL,
  MRS = NULL,
  ...
)

Arguments

object

An object of class 'jjm.output'
Projections

Logical. Whether to include projection tables. Default is FALSE.
Fmult

Optional vector of F multipliers for projections
BiomProj

Optional biomass projection parameters
CapProj

Optional capacity projection parameters
MRS

Optional Maximum Relative Selectivity parameters
...

Additional arguments passed to internal plotting functions

Value

An object of class 'summary.jjm.output' containing tables and plots

Examples

## Not run: 
model <- read.jjm("path/to/model")
model_summary <- summary(model, Projections = TRUE)
print(model_summary)

## End(Not run)

ggplot2 theme for jjmR

Description

ggplot2 theme for jjmR

Usage

theme_jjm(base_size = 12, ...)

Arguments

base_size

Base font size.
...

Additional arguments passed to [ggplot2::theme_bw()].

Value

a ggplot2 theme object

Examples

library(ggplot2)
ggplot(mtcars, aes(mpg)) + geom_histogram() + theme_jjm()

Tidy results of JJM model

Description

Tidy results of JJM model

Usage

tidy_JJM(models)

Arguments

models

an object of class jjm.output

Value

a list of tidy dataframes

Examples

## Not run: 
mod0.00 <- readJJM("h2_0.00", path = "config", input = "input")
tidy_jjm_results <- tidy_JJM(mod0.00)


## End(Not run)

Write dat and ctl files from a JJM model stored in R

Description

Function write to the disk dat and ctl files

Usage

writeJJM(object, path, ...)

Arguments

object

An object of class jjm.config or jjm.output.
path

Directory where the configuration files will be written.
...

Additional arguments

Examples

## Not run: 
writeJJM(mod1)

## End(Not run)