arealutils

Installation

This R package is being developed in support of the analysis in beyond-borders. For this reason, many of the functions are relatively unlikely to be of great general use. This disclaimer given, the package can be installed via:

devtools::install_github("athowes/arealutils")

TMB and rstan

This package uses compiled models from both TMB and rstan. To do this we make use of the very helpful TMBtools and rstantools to set-up the package.

Guidelines for adding a new TMB model

See here.

1. Create model.hpp in arealutils/src/TMB
2. Run TMBtools::export_models()
3. Run devtools::install() to install the package locally

Guidelines for adding a new rstan model

See here.

1. Create model.stan in arealutils/inst/stan
2. Run pkgbuild::compile_dll() to perform a fake R CMD install
3. Run devtools::install() to install the package locally

Models

Model	TMB	aghq	tmbstan	R-INLA	rstan
Constant	✓	✓	✓	✓	→
Independent and identically distributed	✓	✓	✓	✓	→
Besag	✓	✓	✓	✓	→
Besag-York-Mollié 2	✓	✓	✓	✓	→
Centroid kernel (fixed lengthscale)	✓	✓	✓	✓	→
Integrated kernel (fixed lengthscale)	✓	✓	✓	✓	→
Centroid kernel	✓	✓	✓	-	→
Integrated kernel	✓	✓	✓	-	→

• ✓: done
• →: done but temporarily stored elsewhere (rstan compilation times when building the package slow development)

Common tasks

• To build the website, use pkgdown::build_site()
• To document functions, use devtools::document()

Initialisation

The R code used to initialise this package (much of it perhaps not required!) was:

package_name <- "arealutils"

TMBtools::tmb_create_package(
  path = package_name,
  example_code = TRUE,
  fields = list(
  `Authors@R` = 'person("Your", "Name", email = "valid@email.com", role = c("aut", "cre"))')
)

# R wrapper functions to TMB models
usethis::use_template(
  template = "norm_ADFun.R",
  package = "TMBtools",
  save_as = file.path("R", "norm_ADFun.R"),
  data = list(pkg = package_name)
)

usethis::use_template(
  template = "gamma_ADFun.R",
  package = "TMBtools",
  save_as = file.path("R", "gamma_ADFun.R"),
  data = list(pkg = package_name)
)

# testthat tests
usethis::use_testthat()

usethis::use_package(package = "numDeriv", type = "Suggests")

usethis::use_template(
  template = "test-norm_ADFun.R",
  package = "TMBtools",
  save_as = file.path("tests", "testthat", "test-norm_ADFun.R")
)

usethis::use_template(
  template = "test-gamma_ADFun.R",
  package = "TMBtools",
  save_as = file.path("tests", "testthat", "test-gamma_ADFun.R")
)

# update NAMESPACE and package documentation
pkgbuild::compile_dll() # need to compile src first
devtools::document()

rstantools::use_rstan(pkgdir = ".", license = TRUE, auto_config = TRUE)
rstantools::rstan_config(pkgdir = ".")