test_examples: Test Examples

In poissonconsulting/jaggernaut: Bayesian Analyses using 'JAGS'

Description

Test examples to be run manually by package maintainer.

See Also

jaggernaut

Examples

## Not run: 

library(testthat)

model1 <- jags_model("
model { 
 bLambda ~ dlnorm(0, 10^-2) 
 for (i in 1:length(x)) { 
   x[i] ~ dpois(bLambda) 
 } 
}",
model_id = "First Model")

model2 <- jags_model("
model { 
 bLambda ~ dlnorm(0, 5^-2) 
 for (i in 1:length(x)) { 
   x[i] ~ dpois(bLambda) 
 } 
}",
model_id = "Second Model")

models <- combine(model1, model2)
data <- data.frame(x = rpois(100,1))

analysis <- jags_analysis (model1, data, mode = "paper")
analysis <- jags_analysis (model1, data, mode = "demo")
analysis <- jags_analysis (model2, data, mode = "demo")
analysis <- jags_analysis (models, data, mode = "demo")

registerDoParallel(2) 
expect_warning(opts_jagr(parallel = TRUE))

expect_warning(analysis <- jags_analysis (model1, data, mode = "demo"))
expect_warning(analysis <- jags_analysis (model2, data, mode = "demo"))
expect_warning(analysis <- jags_analysis (models, data, mode = "demo"))

#' # stop cluster if registered parallel backend in windows
if(.Platform$OS.type == "windows") stopImplicitCluster()

expect_true(is_parallel(analysis))

opts_jagr(parallel = FALSE)
registerDoSEQ()

expect_true(is_parallel(analysis))
expect_error(update(analysis))

analysis <- jags_analysis (model1, data, mode = "demo")

analysis <- update(analysis)

expect_false(is_parallel(analysis))

registerDoParallel(4) 
opts_jagr(parallel = TRUE)

analysis <- update(analysis)

expect_false(is_parallel(analysis))

analysis <- jags_analysis (model1, data, mode = "demo")
analysis <- jags_analysis (model2, data, mode = "demo")
analysis <- jags_analysis (models, data, mode = "demo")

#' # stop cluster if registered parallel backend in windows
if(.Platform$OS.type == "windows") stopImplicitCluster()

opts_jagr(parallel = FALSE)
registerDoSEQ()

registerDoParallel(4) 
opts_jagr(parallel = TRUE)

 
mod <- jags_model("
                  model {
                  alpha ~ dunif(-20, 20)
                  beta1 ~ dunif(-10, 10)
                  beta2 ~ dunif(-10, 10)
                  beta3 ~ dunif(-10, 10)
                  sigma ~ dunif(0, 5)
                 
                  for (i in 1:length(Year)) {
                  eps[i] ~ dnorm(0, sigma^-2)
                  eLogC[i] <- alpha + beta1 * Year[i]
                  + beta2 * Year[i]^2 + beta3 * Year[i]^3
                  log(eC[i]) <- eLogC[i] + eps[i]
                  C[i] ~ dpois(eC[i])
                  }
                  }",
 derived_code = "data{
 for (i in 1:length(Year)) {
 log(prediction[i]) <- alpha + beta1 * Year[i]
 + beta2 * Year[i]^2 + beta3 * Year[i]^3
 }
 }",
  random_effects = list(eps = "Year"),
  select_data = c("C","Year*")
  )
 dat <- jaggernaut::falcon
 dat$C <- dat$Pairs
 an <- jags_analysis (mod, dat, mode = "debug")
 an <- jags_analysis (mod, dat, mode = "test")
 an <- jags_analysis (mod, dat, mode = "demo")
 an <- jags_analysis (mod, dat, mode = "explore")
 an <- jags_analysis (mod, dat, mode = "report")
 expect_warning(an <- jags_analysis (mod, dat, mode = "paper"))
 an <- jags_analysis (mod, dat, niters = 10^3)

# stop cluster if registered parallel backend in windows
if(.Platform$OS.type == "windows") stopImplicitCluster()

opts_jagr(parallel = FALSE)
registerDoSEQ()

registerDoParallel(4) 
opts_jagr(parallel = TRUE)

demo(peregrine, ask= FALSE)
demo(hm, ask = FALSE)
demo(fritillary, ask= FALSE)
demo(pinna, ask = FALSE)
demo(tits, ask = FALSE)
demo(p610, ask = FALSE)

# stop cluster if registered parallel backend in windows
if(.Platform$OS.type == "windows") stopImplicitCluster()

opts_jagr(parallel = FALSE)
registerDoSEQ()

## End(Not run)

poissonconsulting/jaggernaut documentation built on Feb. 18, 2021, 11:10 p.m.