Nothing
test_that("inputs are correctly carried through to outputs", {
# Set inputs that will be evaluated
driftHRin <- c(0.12, 4.1)
HRin <- c(.08, 2.999)
ssCin <- 120
ssEin <- 120
ssExtin <- 80
nsimin <- 1
# Run simulation analysis
suppressMessages({
ss <- set_n(
ssC = ssCin,
ssE = ssEin,
ssExt = ssExtin
)
covset1 <- set_cov(
n_cat = 2,
n_cont = 1,
mu_int = c(0, 0.4, 0.4),
mu_ext = c(0.7, 0.4, 0.2),
var = c(1, 1.1, 1),
cov = c(0.5, 0.1, 0.9),
prob_int = c(0.95, 0.54),
prob_ext = c(0.85, 0.54)
)
sample_cov <- simu_cov(
ssObj = ss,
covObj = covset1,
HR = HRin,
driftHR = driftHRin,
nsim = nsimin,
seed = 47
)
evt <- set_event(
event = "weibull",
shape = 0.9,
lambdaC = 0.0135,
beta = 0.5
)
c_int <- set_clin(
gamma = c(2, 3, 16),
e_itv = c(5, 10),
CCOD = "fixed-first",
CCOD_t = 100,
etaC = c(0.02, 0.03),
etaE = c(0.2, 0.3),
d_itv = 2
)
c_ext <- set_clin(
gamma = 10,
CCOD = "event",
CCOD_t = 100,
etaC = 0.05
)
sample_time <- simu_time(
dt = sample_cov,
eventObj = evt,
clinInt = c_int,
clinExt = c_ext,
seed = 47
)
res <- run_mcmc(
dt = sample_time,
set_prior(pred = "all", prior = "gamma", r0 = 1, alpha = c(0, 0)),
n.chains = 2,
n.adapt = 100,
n.burn = 100,
n.iter = 200,
seed = 47
)
res2 <- run_mcmc_p(
dt = sample_time,
set_prior(pred = "all", prior = "gamma", r0 = 1, alpha = c(0, 0)),
n.chains = 2,
n.adapt = 100,
n.burn = 100,
n.iter = 200,
seed = 47,
n.cores = 2
)
summ <- get_summary(res)
summ2 <- get_summary(res2)
})
# Check N input combinations captured correctly
expect_equal(
dim(sample_cov),
c(nsimin*NROW(HRin), NROW(driftHRin))
)
# Check N patients, HR, driftHR captured correctly in simulated data
for(i in 1:dim(sample_cov)[1]) {
for(j in 1:dim(sample_cov)[2]) {
# N patients
expect_equal(
ssCin,
sum(sample_cov[[i,j]][,'ext']==0 & sample_cov[[i,j]][,'trt']==0)
)
expect_equal(
ssEin,
sum(sample_cov[[i,j]][,'ext']==0 & sample_cov[[i,j]][,'trt']==1)
)
expect_equal(
ssExtin,
sum(sample_cov[[i,j]][,'ext']==1 & sample_cov[[i,j]][,'trt']==0)
)
# HR
expect_equal(
rep(HRin,each=nsimin)[i],
unique(sample_cov[[i,j]][,'HR'])
)
# driftHR
expect_equal(
driftHRin[j],
unique(sample_cov[[i,j]][,'driftHR'])
)
}
}
# Check driftHR and HR captured correctly in sample of MCMC outputs
## run_mcmc()
### res
expect_equal(
driftHRin,
unique(res$driftHR)[order(unique(res$driftHR))]
)
expect_equal(
HRin,
unique(res$HR)[order(unique(res$HR))]
)
### summ
expect_equal(
driftHRin,
unique(summ$driftHR)[order(unique(summ$driftHR))]
)
expect_equal(
HRin,
unique(summ$HR)[order(unique(summ$HR))]
)
## run_mcmc_p()
### res
expect_equal(
driftHRin,
unique(res2$driftHR)[order(unique(res2$driftHR))]
)
expect_equal(
HRin,
unique(res2$HR)[order(unique(res2$HR))]
)
### summ
expect_equal(
driftHRin,
unique(summ2$driftHR)[order(unique(summ2$driftHR))]
)
expect_equal(
HRin,
unique(summ2$HR)[order(unique(summ2$HR))]
)
})
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