In jflournoy/permediatr:

library(permediatr)
library(lme4)
attach(list(nreps = 1, nperms = 500, mc.cores = 7, J = 100, n_j = 10, a = 0, b = .5, c_p = 0, theta_ab = .2, optimizer = 'bobyqa'))
adf <- simulate_mediation_data(J = J, n_j = n_j, a = a, b = b, c_p = c_p, theta_ab = theta_ab)
ab_mod <- permediatr::lmemm_within(data = adf,
                                   y.name = 'y',
                                   x.name = 'x_wc',
                                   m_b.name = 'm_wc',
                                   m_a.name = 'm',
                                   group.id = 'id',
                                   covariates.y=c('cov.y', 'm_bc', 'x_bc'),
                                   covariates.m=c('cov.m', 'x_bc'),
                                   random.a=T,
                                   random.b=T,
                                   random.c_p=T, optimizer = optimizer)
ab <- indirectEffect(ab_mod)

boot_rez <- permediatr::run_simulation(3, niter = 500, mc.cores = 7, simtype = 'bootstrap', J = 100, n_j = 10, a = 0, b = 0, c_p = 0, theta_ab = .2, optimizer = 'bobyqa', re.form = NA, boottype = 'parametric')
data.table::rbindlist(lapply(boot_rez, as.data.frame))

system.time({oneboot <- permediatr::boot_ab(ab_mod, nsim = 250, ncpus = 7, re.form = NA, type = 'cases', how = 'both', seed = 1)})
twoboot <- permediatr::boot_ab(ab_mod, nsim = 1000, ncpus = 7, re.form = NA, type = 'cases', how = 'both', seed = 1)
threeboot <- permediatr::boot_ab(ab_mod, nsim = 1000, ncpus = 7, re.form = NA, type = 'cases', how = 'both', seed = 123123)
rbind(summary(oneboot),summary(twoboot), summary(threeboot))

do.call(rbind, list(summary(oneboot, 'ab'), summary(oneboot, 'a'), summary(oneboot, 'b')))

jflournoy/permediatr documentation built on Dec. 10, 2019, 11:34 a.m.