# DEMO FOR SEMTREE


require("semtree")
require("lavaan")

# ORGANIZE DATA BY TYPE FOR COVARIATES.
# SOME COVARIATES ARE ORGANIZED IN THE DATA. MODEL VARIABLES AND 
# COVARIATES 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 ~ mui*1;
g1 ~~ g1; g1 ~ sli*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 <- semtree.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.

controlOptions$alpha <- 0.01

# RUN TREE.

tree <- semtree(model=lgcModel, data=lgcm, control = controlOptions)

# SEE PLOT.
# THE PLOT FUNCTION WILL SHOW ALL FREE PARAMETERS AT EACH TERMINAL NODE.
# THIS CAN CREATE UNREADABLE FIGURES FOR MODELS WITH MANY FREE PARAMETERS.

plot(tree)

# SEE SUMMARY.
# OVERALL MODEL FACTS ARE GIVEN WITH THE SUMMARY FUNCTION.

summary(tree)

# summary(treeConstrained)

# USING THE PRINT FUNCTION WILL PROVIDE AN OVERVIEW OF THE MODEL
# SPLITS, LR TESTS WITH DF, AND SUBGROUP SIZES (N).

print(tree)

# GET NODE PARAMETERS (leafs only as default).
# THE DEFAULT IS ONLY DISPLAYING LEAF NODE PARAMETER ESTIMATES.

parameters(tree)

# TO GET ALL PARAMETER ESTIMATES FOR EVERY NODE CHANGE THE DEFAULT TO.

parameters(tree, leafs.only=FALSE)

# SUBTREE FUNCTION.
# IF ONLY A SUBSET OF THE TREE IS TO BE EXAMINED, THEN THE TREE CAN 
# BE PARED. THIS IS DONE WITH A SUBSET FUNCTION WHICH STORES THE TREE
# FROM A GIVEN NODE ON. IF THE TREE FROM NODE 2 ON IS DESIRED, THEN:

treeSub <- subtree(tree, startNode=3)


# ALTERNATIVE SPLIT RULE

controlOptions$method <- "fair"
tree2 <- semtree(model=lgcModel, data=lgcm, control = controlOptions)

# disabled for time restrictions on CRAN
#controlOptions$method <- "cv"
#tree3 <- semtree(model=lgcModel, data=lgcm, control = controlOptions)