demo/semforestLGCModellavaan.R

In semtree: Recursive Partitioning for Structural Equation Models

# DEMO FOR SEMTREE


require("semtree")
require("lavaan")
require("future")
plan(sequential)

# ORGANIZE DATA BY TYPE FOR COVARIATES.
# SOME COVARIATES ARE ORGANIZED IN THE DATA. MODEL VARIABLES AND 
# CAOVARIATES DO NOT NEED TO BE ORDERED IN THE DATASET. ONLY VARIABLE
# TYPE NEEDS TO BE DEFINED FOR THE COVARIATES (FACTOR/ORDERED/NUMERIC)
# BE AWARE OF THE EXPONENTIAL GROWTH OF MODEL COMPARISON WITH INCREASES
# IN NUMBER OF FACTORS PER A COVARIATE.

data(lgcm)

lgcm$agegroup <- as.ordered(lgcm$agegroup)
lgcm$training <- as.factor(lgcm$training)
lgcm$noise <- as.numeric(lgcm$noise)

# LOAD IN LAVAAN MODEL.
# A SIMPLE LINEAR GROWTH MODEL WITH 5 TIME POINTS FROM SIMULATED DATA

lgcModelstr <- '
g0 =~ 1*o1 + 1*o2 + 1*o3 + 1*o4 + 1*o5;
g1 =~ 0*o1 + 1*o2 + 2*o3 + 3*o4 + 4*o5;
g0 ~~ g0; g0 ~ 1;
g1 ~~ g1; g1 ~ 1;
g0 ~~ g1;
o1 ~~ o1; o1 ~ 0*1;
o2 ~~ o2; o2 ~ 0*1;
o3 ~~ o3; o3 ~ 0*1;
o4 ~~ o4; o4 ~ 0*1;
o5 ~~ o5; o5 ~ 0*1;
'
lgcModel <- lavaan(lgcModelstr, lgcm, do.fit=TRUE)

# TREE CONTROL OPTIONS.
# TO OBTAIN BASIC/DEFAULT SMETREE OPTIONS, SIMPLY TPYE THE FOLLOWING:

controlOptions <- semforest.control()

# THE CONTENTS OF THE DEFAULT CONTROLS CAN THEN BE VIEWED.

controlOptions

# AND MODEL OPTIONS CAN BE CHANGED BY REDEFINING ELEMENTS OF THE 
# CONTROL OBJECT.



# RUN TREE.

forest <- semforest(model=lgcModel, data=lgcm,control = controlOptions)

# VARIABLE IMPORTANCE

vim <- varimp(forest)

plot(vim)

# PARTIAL DEPENDENCE

pd <- partialDependence(forest, "agegroup", "g0~1")  # g0 ~1
plot(pd)