ageproR

ageproR is a developing R-package designed to handle input data to and from AGEPRO (Age Structured Projection Model) calculation engine.

Important

If you using AGEPRO for production, please use:

• AGEPRO-GUI, includes binary for AGEPRO calculation engine
• AGEPRO Command Line based Calculation Engine source code repo

Note

ageproR is still in development. These features will be implemented in future updates.

• Predictor Recruitment Models
• Fixed Recruitment Model
• Empirical Cumulative Distribution Factor for w/ Linear Decline to Zero
• Markov Matrix Recruitment Model
• Run AGEPRO models with the AGEPRO calculation engine within R.
• Exported AGEPRO output R data objects.

Importing Stock Synthesis report data as AGEPRO input data is being developed as a separate R-package: ss3agepro

Installation

You can install the development version of ageproR from NOAA Fisheries OST Repository with:

# via `pak`
install.packages("pak")
pak::pkg_install("nmfs-ost/ageproR")

# alternative method
install.packages("remotes")
remotes::install_github("nmfs-ost/ageproR")

AGEPRO input file format

ageproR is compatible with the AGEPRO input file formats AGEPRO VERSION 4.0 & AGEPRO VERSION 4.25. By default, ageproR saves to the AGEPRO VERSION 4.25 Input File Format.

Please refer to the AGEPRO Reference Manual for more technical details.

Agepro Model Workflow Examples

Setting up a new agepro_inp_model

library("ageproR")

# Load path of ageproR's included Example_UKU Input File
inpfile <- file.path(find.package("ageproR"),"example/Example_UKU.INP")

# Load path of ageproR's included Example_UKU Bootstrap File
bsnfile <- file.path(find.package("ageproR"),"example/Example_UKU.BSN")

# Create a agepro_inp_model with default values
test <- ageproR::agepro_inp_model$new()
# By Default, creating a new instance of agepro_inp_model with default values will include a 
# single "NULL Recritment Model", a placeholder recruitment model. It will print a WARNING 
# to replace this Model with a vaild recruitment model before saving to file. AGEPRO  
# Calcuation Engine will not recognize NULL Recruitment models.

# Set model with Recruit Model 14: "Empirical Cumulative Distribution Function of Recruitment". 
test$set_recruit_model(c(14))

# New agepro_models instances return NULL
test$bootstrap$bootstrap_file

# Set Path of Bootstrap File 
# Note: Leaving parameter blank may request a file dialog window.
test$set_bootstrap_filename(bsnfile)

Setting up a new agepro_inp_model w/ multiple recruitment models

# New instance of agepro_inp_model refreses class to default values.
# Specify the "number of recuitment models" (num_rec_models) at initializtion
test <- ageproR::agepro_inp_model$new(num_rec_models=3)

# Multiple recruitments depend on agepro_model's "number of recruitment models". 
# For example, to set a 3 recruit agepro_inp_model w/ two Beverton-Holt models and a single
# Ricker model:
test$set_recruit_model(c(5,5,6)) 
# NOTE: A valid rerun of set_recruit_model will OVERWRITE the previous [RECRUIT] values.

Reading or importing from AGEPRO input file (*.inp)

Note

Loading AGEPRO Input Files with multiple recuitment models will automatically set the number of recruits and overwrite the existing model’s recruitment data; For instance, reading a AGEPRO input file with multiple recruits will overwrite newly created model’s default data single NULL Recruitment.

# New instance of agepro_inp_model refreses class to default values.
test2 <- ageproR::agepro_inp_model$new()

# Importing AGEPRO input file. 
# Leaving parameter blank may request a file dialog window.
test2$read_inp(inpfile) 

# Note: Input Files with the `AGEPRO VERSION 4.0` format can be loaded to ageproR currently, 
# but will be deprecated. In future updates. By default, AGPRO input files will be saved in the 
# `AGEPRO VERSION 4.25` format. 
# Function `read_inp` will also detect non-existant bootstrap paths. If there are no warnings, 
# check the agepro model's bootstrap filepath equals the intended "bsnpath". If not: 
# test2$set_bootstrap_filename(bsnfile)

Saving to AGEPRO Input File.

# Using the "test2" model .... 
# Using tempfile() as example filepath
outfile <- tempfile("example1_", fileext = ".inp")

# Note: Leaving parameter blank may request a file dialog window.  
test2$write_inp(outfile)

Citation

Please cite this AGEPRO project as:

Brodziak, Jon and Rago, Paul J. and Conser, Ramon. (1998). A General Approach for Making Short-Term 
Stochastic Projections from an Age-Structured Fisheries Assessment Model. Fishery Stock Assessment 
Models, 933–954. https://doi.org/10.4027/fsam.1998.52

The following BibTeX entry can be copied and used in a .bib file:

@article{article,
author = {Brodziak, Jon and Rago, Paul J. and Conser, Ramon},
year = {1998},
month = {01},
pages = {933-954},
title = {A General Approach for Making Short-Term Stochastic Projections from an Age-Structured Fisheries Assessment Model},
isbn = {9781566120579},
doi = {10.4027/fsam.1998.52}
}

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Disclaimer

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U.S. Department of Commerce | National Oceanographic and Atmospheric Administration | NOAA Fisheries