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: 2025-03-03 05:19:51 UTC
Source: https://github.com/SPRFMO/jjmr

Help Index

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)

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)

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)

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)

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)

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, refpt = NULL)

Arguments

mod

jjm object that is a list of lists
refpt

A number 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)

Value

A model

Examples

# fixed_bmsy(mod_h1_1.00, refpt=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

Value

an object subset to matches in names with strings

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.
...

Additional parameters passed to plot.

Examples

## Not run: 
kobe(model)

## End(Not run)

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)

Value

a ggplot2 plot object

Examples

## Not run: 

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


## End(Not run)

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.

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)

ggplot2 theme for jjmR

Description

ggplot2 theme for jjmR

Usage

theme_jjm(base_size = 14, ...)

Arguments

...

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)