inst/tinytest/test-glmm_poisson.r

In depower: Power Analysis for Differential Expression Studies

library(tinytest)

#-------------------------------------------------------------------------------
# Data
#-------------------------------------------------------------------------------
set.seed(1234)
d <- sim_bnb(
  n = 40,
  mean1 = 10,
  ratio = 1.5,
  dispersion = 2
)

lrt <- glmm_poisson(d, test = "lrt", ci_level = 0.95)
wald <- glmm_poisson(d, test = "wald", ci_level = 0.95)

#-------------------------------------------------------------------------------
# Structure
#-------------------------------------------------------------------------------
expect_equal(
  lrt,
  list(chisq = 32.525582707165, df = 1L, p = 1.17633805049949e-08,
    ratio = list(estimate = 1.45336781526169, lower = 1.27717807844155,
        upper = 1.65542865749175), mean1 = list(estimate = 6.89552391371006,
        lower = 5.08790784218065, upper = 9.20682992879782),
    mean2 = list(estimate = 10.0217325255535, lower = 6.49816436116398,
        upper = 15.2412501087846), item_sd = list(estimate = 0.850882520374344,
        lower = 0.655998178980542, upper = 1.10366322144939),
    n1 = 40L, n2 = 40L, method = "GLMM for two dependent Poisson ratio of means",
    test = "lrt", alternative = "two.sided", ci_level = 0.95,
    hessian = "Hessian appears to be positive definite.",
    convergence = "relative convergence (4)"),
  tolerance = 0.0001,
  scale = 1
)

expect_equal(
  wald,
  list(chisq = 31.9648555673617, df = 1L, p = 1.5698720626369e-08,
    ratio = list(estimate = 1.45336781526169, lower = 1.27668983158746,
        upper = 1.65449583303417), mean1 = list(estimate = 6.89552391371006,
        lower = 5.16226787476225, upper = 9.2107289273006), mean2 = list(
        estimate = 10.0217325255535, lower = 6.59061490363958,
        upper = 15.2391126294261), item_sd = list(estimate = 0.850882520374344,
        lower = 0.655998178980542, upper = 1.10366322144939),
    n1 = 40L, n2 = 40L, method = "GLMM for two dependent Poisson ratio of means",
    test = "wald", alternative = "two.sided", ci_level = 0.95,
    hessian = "Hessian appears to be positive definite.",
    convergence = "relative convergence (4)"),
  tolerance = 0.0001,
  scale = 1
)