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library(glmmTMB)
library(testthat)
data("sleepstudy", package = "lme4")
pp <- list(beta = c(280, 3),
betadisp = 1,
theta = c(3, 0.5, 2))
s1 <- simulate_new( ~ Days + (Days|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp)[[1]]
test_that("basic simulate_new", {
expect_equal(head(s1),
c(273.908009267299, 278.879666041338, 274.760596391018, 283.450108370691,
286.469055736181, 290.145189139373))
})
test_that("basic simulate_new, returning object", {
s2 <- simulate_new( ~ Days + (Days|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp,
return_val = "object")
expect_equal(fixef(s2)$cond,
c(`(Intercept)` = 280, Days = 3))
expect_equal(c(VarCorr(s2)$cond$Subject),
rep(c(exp(3*2), exp(3)*exp(0.5)*2/sqrt(2^2+1), exp(0.5*2)), times = c(1, 2, 1)))
## SDs are exp(3), exp(0.5), cor is 2/(sqrt(2^2 +1)
expect_equal(unname(head(getME(s2, "b"))),
c(-0.837259673343575,
6.24196658894249, 1.32388051566616,
12.4287264928693, 0.829382894489882,
18.4190056),
tolerance = 1e-7)
})
s3 <- simulate_new( ~ Days + (Days|Subject),
newdata = sleepstudy,
seed = 101,
family = gaussian,
newparams = pp,
return_val = "pars")
test_that("simulate_new, returning pars", {
## FIXME: would be nice to have params in the canonical order
})
### now work on fixing particular elements ...
pp2 <- c(pp, list(b = rep(c(-1, 0, 1), length.out = 36)))
s4 <- simulate_new( ~ Days + (Days|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp2)[[1]]
test_that("simulate_new with specified b (values)", {
## should be different from random-b sim
expect_false(isTRUE(all.equal(s1, s4)))
})
## need this for a downstream example
s5 <- simulate_new( ~ Days + (Days|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp2,
return_val = "pars")
test_that("simulate_new with specified b (pars)", {
expect_identical(unname(s5[names(s5)=="b"]), pp2$b)
})
test_that("simulate_new with specified b (object)", {
s6 <- simulate_new( ~ Days + (Days|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp2,
return_val = "object")
expect_identical(unname(getME(s6, "b")),
## correct, although names are wrong?
pp2$b)
})
pp3 <- c(pp, list(b = list("Days|Subject" = pp2$b)))
test_that("simulate_new with specified b (pars, b as list)", {
s7 <- simulate_new( ~ Days + (Days|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp3,
return_val = "pars")
expect_identical(unname(s5[names(s5)=="b"]), pp3$b[["Days|Subject"]])
})
pp4 <- list(beta = c(280),
betadisp = 1,
theta = c(-1, 1, 0))
s8 <- simulate_new( ~ 1 + (1|Subject) + ar1(0+factor(Days)|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp4)[[1]]
s9 <- simulate_new( ~ 1 + (1|Subject) + ar1(0+factor(Days)|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp4,
return_val = "pars")
test_that("simulate_new with two RE terms", {
expect_equal(unname(head(s9)),
c(-0.119942121932298, 0.203239358640131, -0.248297964136576,
0.078858438002708, 0.114325605998615, 0.431878061822679))
})
nb <- sum(names(s9) == "b")
pp5 <- c(pp4, list(b = rep(c(-1, 0, 1), length.out = nb)))
s10 <- simulate_new( ~ 1 + (1|Subject) + ar1(0+factor(Days)|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp5)[[1]]
test_that("simulate_new with two RE terms, fixed b", {
s11 <- simulate_new( ~ 1 + (1|Subject) + ar1(0+factor(Days)|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp5, return_val = "pars")
expect_equal(unname(s11[names(s11) == "b"]), pp5$b)
})
ns <- length(unique(sleepstudy$Subject))
pp6 <- c(pp4, list(b = list("0+factor(Days)|Subject" =
rep(c(-1, 0, 1), length.out = nb - ns))))
s12 <- simulate_new( ~ 1 + (1|Subject) + ar1(0+factor(Days)|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp6)[[1]]
test_that("simulate_new, b partially fixed", {
expect_false(isTRUE(all.equal(s10, s12)))
})
s13 <- simulate_new( ~ 1 + (1|Subject) + ar1(0+factor(Days)|Subject),
seed = 101,
newdata = sleepstudy,
family = gaussian,
newparams = pp6,
return_val = "pars")
test_that("simulate_new, b partially fixed (pars)", {
bvec <- unname(s13[names(s13) == "b"])
expect_equal(head(bvec),
c(-0.119942121932298, 0.203239358640131, -0.248297964136576,
0.078858438002708, 0.114325605998615, 0.431878061822679))
expect_identical(bvec[-(1:ns)], pp6$b[[1]])
})
## s14 <- simulate_new( ~ 1 + (1|Subject) + ar1(0+factor(Days)|Subject),
## seed = 101,
## newdata = sleepstudy,
## family = gaussian,
## newparams = pp6,
## return_val = "object")
## Problem with these parameter entries:
## b
## 3
## Error in MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, :
## Only numeric matrices, vectors and arrays can be interfaced
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