Nothing
context("Step 3 - running BAnOCC")
load("testthat_objects/banocc_model_test.RData")
load("testthat_objects/sample_stan_data.RData")
test_that("get_gamma_param gives error if param <= 0", {
err_string <- "must be > 0"
expect_error(get_gamma_param(0, "a"), err_string)
expect_error(get_gamma_param(-1, "a"), err_string)
})
test_that("get_gamma_param returns param if param > 0", {
expect_equal(get_gamma_param(pi, "a"), pi)
expect_equal(get_gamma_param(2, "a"), 2)
})
n <- rep(0, Data$P)
L <- 10 * diag(Data$P)
init1 <- list(list(m = n, O=diag(Data$P), lamda=0.02))
init2 <- NULL
init_opt <- list(init1, init2)
use_matrix <- list(TRUE, FALSE)
opt_idx <- expand.grid(init = seq_along(init_opt),
use_matrix = seq_along(use_matrix))
all_args <- lapply(seq_len(nrow(opt_idx) * 2), function(i){
j <- ifelse(i %% 2 == 0, i / 2, (i + 1) / 2)
idx <- c(opt_idx$init[j],
opt_idx$use_matrix[j])
args <- list(init=init_opt[[idx[1]]],
use_matrix=use_matrix[[idx[2]]])
return(args)
})
sw_run_banocc <- function(use_matrix=FALSE, init=NULL){
sink("banocc.out", type="output")
if (use_matrix){
data <- as.matrix(Data$C)
} else {
data <- as.data.frame(Data$C)
}
rb <- suppressWarnings(run_banocc(
compiled_banocc_model=compiled_banocc_model, C=data, a=0.5,
b=0.01, n=n, L=L,
chains=1, iter=4, warmup=2, init=init,
verbose=FALSE, num_level=0
))
sink()
return(rb)
}
on_cran <- !identical(Sys.getenv("NOT_CRAN"), "true")
on_bioc <- !identical(Sys.getenv("BBS_HOME"), "")
if (!on_cran && !on_bioc){
rb <- lapply(seq_along(all_args), function(i){
do.call(what=sw_run_banocc, args=all_args[[i]])
})
}
test_that("run_banocc returns a list", {
skip_on_cran()
skip_on_bioc()
for (i in seq_along(rb)){
expect_is(rb[[i]], "list")
}
})
test_that("run_banocc takes a matrix", {
skip_on_cran()
skip_on_bioc()
for (i in seq_along(rb)){
if (all_args[[i]]$use_matrix){
expect_is(rb[[i]], "list")
}
}
})
test_that("run_banocc takes a data frame", {
skip_on_cran()
skip_on_bioc()
for (i in seq_along(rb)){
if(!all_args[[i]]$use_matrix){
expect_is(rb[[i]], "list")
}
}
})
rb_names <- c("Data", "Fit")
test_that("run_banocc returns list with correct names", {
skip_on_cran()
skip_on_bioc()
for (i in seq_along(rb)){
expect_equal(sort(names(rb[[i]])), sort(rb_names))
}
})
test_that("run_banocc Data elt is list", {
skip_on_cran()
skip_on_bioc()
for (i in seq_along(rb)){
expect_is(rb[[i]]$Data, "list")
}
})
data_names <- c("C", "N", "P", "n", "L", "a", "b")
test_that("run_banocc Data elt has correct names", {
skip_on_cran()
skip_on_bioc()
for (i in seq_along(rb)){
expect_equal(sort(names(rb[[i]]$Data)), sort(data_names))
}
})
test_that("run_banocc Fit elt is stanfit object", {
skip_on_cran()
skip_on_bioc()
for (i in seq_along(rb)){
expect_is(rb[[i]]$Fit, "stanfit")
}
})
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