#SCoA bifactor

#install required libraries
library(lavaan)
library(semPlot)
#to create bifactor 8 factor SCoA model
SCoA6bf.model <- '
BD =~ bd1 + bd2 + bd3 + bd4 + bd5
IG =~ ig1 + ig2 + ig3
SI =~ si1 + si2 + si3 + si4 + si5
TI =~ ti1 + ti2 + ti3 + ti4 + ti5 + ti6 
CE =~ ce1 + ce2 + ce3 + ce4 + ce5 + ce6
PE =~ pe1 + pe2
SQ =~ sq1 + sq2
SF =~ sf1 + sf2 + sf3
general =~ bd1 + bd2 + bd3 + bd4 + bd5 + ce1 + ce2 + ce3 + ce4 + ce5 + ce6 + ig1 + ig2 + ig3 + pe1 + pe2 + sf1 + sf2 + sf3 + sf4 + si1 + si2 + si3 + si4 + si5 + sq1 + sq2 + ti1 + ti2 + ti3 + ti4 + ti5 + ti6

# specific factors are uncorrelated with general factor
     general ~~ 0*BD + 0*CE + 0*IG + 0*PE + 0* SF + 0*SI + 0*SQ +0*TI
'

#to create bifactor 4 main factors (join IG, BD) SCoA model
SCoA6bf3.model <- '
BD =~ bd1 + bd2 + bd3 + bd4 + bd5 + ig1 + ig2 + ig3
IMP =~ si1 + si2 + si3 + si4 + si5 + ti1 + ti2 + ti3 + ti4 + ti5 + ti6 
AFFECT =~ ce1 + ce2 + ce3 + ce4 + ce5 + ce6 + pe1 + pe2
EXTRNL =~ sq1 + sq2 + sf1 + sf2 + sf3
general =~ bd1 + bd2 + bd3 + bd4 + bd5 + ce1 + ce2 + ce3 + ce4 + ce5 + ce6 + ig1 + ig2 + ig3 + pe1 + pe2 + sf1 + sf2 + sf3 + sf4 + si1 + si2 + si3 + si4 + si5 + sq1 + sq2 + ti1 + ti2 + ti3 + ti4 + ti5 + ti6

# specific factors are uncorrelated with general factor
     general ~~ 0*BD + 0*IMP + 0*AFFECT + 0*EXTRNL
'

#do bifactor CFA analysis of model
SCoAbf3_fit <- cfa (SCoA6bf3.model, data=NZSCoAVI, control=list(iter.max=100000))
#get results of bifactor cfa
summary (SCoAbf3_fit, standardized=TRUE)
fitmeasures(SCoAbf3_fit)

#to get gamma hat fit index
library(semTools)
moreFitIndices(SCoAbf3_fit)

#to get x2/df ratio and p-value-thanks to Terry Jorgensen UvA (amsterdam)
fm <- fitMeasures(SCoAbf3_fit)
fm[["chisq"]] / fm[["df"]]
fm["pvalue"] 

#to get conventional correlated factors diagram
semPaths(SCoAbf3_fit, intercept = FALSE, whatLabel = "std",  residuals = FALSE, exoCov = TRUE) 
#this design separates sempaths properly
semPaths(SCoAbf3_fit, "model", "std", bifactor = "g", layout = "tree2", residuals = FALSE, exoCov = FALSE)

#to get lavaanplot style chart
library(LavaanPlot)
lavaanPlot(model = SCoAbf3_fit, node_options = list(shape = "box", fontname = "Helvetica"), edge_options = list(color = "grey"), coefs = TRUE, covs = TRUE, stars = TRUE)