neusDFA:

######################
# Simulate data for a linear mixed model with random intercepts
######################

set.seed(1)
Factor = rep( 1:10, each=10)
Z = rnorm( length(unique(Factor)), mean=0, sd=1)

X0 = 0
Y = Z[Factor] + X0 + rnorm( length(Factor), mean=0, sd=1)

######################
# Run in TMB
######################

install.packages("TMB", type = 'source')
library(TMB)
Version = "linear_mixed_model"

# Sys.setenv(PATH = paste("C:/Rtools/bin", Sys.getenv("PATH"), sep=";"))
# Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")

# Download CPP file
setwd( tempdir() )
download.file( url="https://raw.githubusercontent.com/James-Thorson/mixed-effects/master/linear_mixed_model/linear_mixed_model.cpp", destfile="linear_mixed_model.cpp", method="auto")
compile( paste0(Version,".cpp") )

# Generate inputs for TMB
Data = list( "n_data"=length(Y), "n_factors"=length(unique(Factor)), "Factor"=Factor-1, "Y"=Y)
Parameters = list( "X0"=-10, "log_SD0"=2, "log_SDZ"=2, "Z"=rep(0,Data$n_factor) )
Random = c("Z")

# Build TMB object
dyn.load( dynlib(Version) )
Obj = MakeADFun(data=Data, parameters=Parameters, random=Random)  #

# Check that TMB is working
Obj$fn( Obj$par )