README.md

In allen-chen-noaa-gov/barebones.FishSET: Barebones discrete choice modeling

Barebones FishSET

This is a barebones version of the FishSET package, primarily used for directly calling some of the lower-level functions.

Installation

To install with vignette:

install.packages("devtools") library(devtools)

Set the directory you've downloaded the package into:

setwd("J:/Fishperson/Directory_containing_barebones.FishSET")

Install with vignettes:

install("barebones.FishSET", build_vignettes = TRUE)

Check out documentation and vignette:

help(package="barebones.FishSET") vignette("barebones.FishSET.vignette", package="barebones.FishSET")

Please see vignette for usage examples.

You can create a stand-alone .html vignette by then running:

setwd("barebones.FishSET") devtools::build_vignettes()

Reproducible example

The code used to reproduce the work in "Chen, Y. Allen, Alan C. Haynie, and Christopher M. Anderson. 2023. Journal of the Association of Environmental and Resource Economists." can be found below. This also serves as an use example of the package. Please note the package functions should be generalizable to any discrete choice problem - please see vignette for examples.

library(barebones.FishSET)
library(dplyr)
library(doParallel)
library(foreach)

# check how many workers your machine has
# registerDoParallel(cores = )

# number of observations per location
iinum <- rep(1000, 4)
# number of MC iterations
mcnum <- 100
# no constant model no kernel
constp <- rep(0, 4)
bwnum <- -1

# GEV choice error
sertype <- "gev"
chodev <- 1

# utility and catch parameters
alpha <- 3
betac <- -1
regconstant <- 0

# set a directory here
# dirout <- paste0()

for (it in seq(1, 4, by = 0.5)) {

# run a model for each catch deviation
cdev <- it

# about 3 hours each with 8 workers
print(Sys.time())
par_res_base <- foreach(nn = 1:(mcnum), .packages = c("barebones.FishSET",
    "dplyr")) %dopar% mc_func_base(nn, constp, cdev, iinum, bwnum, sertype,
    chodev, alpha, betac, regconstant)
print(Sys.time())

saveRDS(par_res_base, paste0(dirout, "MC_", cdev, ".rds"))

}

# this model is for the base case with no private information
cdev <- 0

print(Sys.time())
par_res_base <- foreach(nn = 1:(mcnum), .packages = c("barebones.FishSET",
    "dplyr")) %dopar% mc_func_true(nn, constp, cdev, iinum, bwnum, sertype,
    chodev, alpha, betac, regconstant)
print(Sys.time())

saveRDS(par_res_base, paste0(dirout, "MC_", cdev, ".rds"))

The code to reproduce the simulation figures is included as a script. These produce figures 1 through 3. Please see MC_make_figs.r in the exec folder. The code to run the empirical example is also included as a script, however, the confidential data used to run the empirical example is not included. Please see Emp_ex.r in the exec folder.

DISCLAIMER

“This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.”

allen-chen-noaa-gov/barebones.FishSET documentation built on March 1, 2024, 8:19 a.m.