examples_tests/ex_for_kara2.R

In jlstiles/SDE_transport: SDEtransportsim

# devtools::install_github("jeremyrcoyle/sl3")
# devtools::install_github("jlstiles/SDE_transport")
library("SDEtransportsim")
library("parallel")
library("doParallel")

#Set up data generating process:
# data(example_dgp)
# data = data_example

truth = list(
  f_W = function(n) {
  W1 = rnorm(n)
  W2 = rnorm(n)
  data.frame(W1=W1, W2=W2)
}
,f_S = function(W) {
  with(W, plogis(-.37*W1 + W2-.17))
}

,f_A = function(S,W) {
  rep(.5, length(S))
}

,f_Z = function(A,S,W) {
  df = as.data.frame(cbind(W, A = A))
  with(df, plogis(.3*S*(.4*W1 - W2 + A) +.4*W1 -.6*W2 + 1*A -.5*S + .3))
}

,f_M = function(Z,W,S) {
  df = as.data.frame(cbind(Z=Z, W, S))
  with(df, plogis(.4*S*(1*W1 +.6*W2 - 1*Z) + .41*W1 +.16*W2 - 3*Z + .51*S + 1.6))
}

,f_Y = function(M,Z,W) {
  df = as.data.frame(cbind(M = M, Z = Z, W))
  with(df, plogis(W2 + W1 - Z + 2*M - .4))
}
)

truth_NT = list(
  f_W = function(n) {
  W1 = rnorm(n)
  W2 = rnorm(n)
  data.frame(W1=W1, W2=W2)
}

,f_A = function(W) {
  if (is.vector(W)) nn = length(W) else nn = nrow(W)
  rep(.5, nn)
}

,f_Z = function(A,W) {
  df = as.data.frame(cbind(W, A = A))
  with(df, plogis(.4*W1 -.6*W2 + 1*A + .3))
}

,f_M = function(Z,W) {
  df = as.data.frame(cbind(Z=Z, W))
  with(df, plogis(.41*W1 +.16*W2 - 3*Z+ 1.6))
}

,f_Y = function(M,Z,W) {
  df = as.data.frame(cbind(M = M, Z = Z, W))
  with(df, plogis(W2 + W1 - Z + 2*M - .4))
}
)

# be sure of no bad positivity
n=100000
W = truth$f_W(n)
hist(truth$f_S(W))
S = rbinom(n,1,truth$f_S(W))
A = rbinom(n, 1, .5)
hist(truth$f_Z(A,S,W), breaks = 200)
Z = rbinom(n,1,truth$f_Z(A,S,W))
hist(truth$f_M(Z,W,S), breaks = 200)
M = rbinom(n,1,truth$f_M(Z,W,S))
# forms for non-transporting
formsNT=list(Aform = formula("A ~ W1 + W2"),
             Zstarform = formula("Z ~  A + W1 + W2"),
             QZform = formula("Qstar_Mg ~ W1 + W2"),
             Mstarform = formula("M ~ Z + W1 + W2"),
             Yform = formula("Y ~ M + Z + W1 + W2"))


Wnames = c("W1", "W2")
Wnamesalways = c("W1")

n=1e5
data = gendata.SDEtransport(n, truth$f_W, truth$f_S, truth$f_A, truth$f_Z, truth$f_M, truth$f_Y)

data$weights = rep(1,nrow(data))

dataNT = data[data$S==0,]
dataNT$S = NULL

testNT = SDE_tmle_lasso(dataNT, formsNT, RCT = 0.5, Wnames = Wnames, Wnamesalways = Wnamesalways, 
                        transport = FALSE, pooled = FALSE, gstar_S = 0, truth = truth_NT) 

testNT
# All should be the same
check_truth = check_sim(1e5, truth, truth_NT)