rm(list=ls())
library(permuco)
library(Matrix)
library(MASS)
library(combinat)
library(profvis)
devtools::install_github("jaromilfrossard/permucoQuasiF")
#devtools::install_github("jaromilfrossard/gANOVA")
Sys.setenv(LANG = "en")
dir= ""
#### simulation type
## decreasing variance through interaction
## increasing variable through interaction
## Large variance for id:item
##
t0 = proc.time()
#setwd(dir)
lf= list.files(paste(dir,"function_data",sep=""))
for(lfi in lf){
print(lfi)
source(paste(dir,"function_data/",lfi,sep=""))
}
ni= 18 #18
ns = 18#16
na =list(S = 3,I =3, C =2, SI = 1, O = 1, R = 1)
fseed = 42
source(paste("data_uni_lmm.R",sep=""))
f_s = subject~(fI*fC)
f_i = item~(fS*fC)
f_si = (subject_item)~(fC)
zl_s = Zlist(f_s,df)
scale_s = scalelist(Zlist = zl_s,type="flat")
omega_glist_s = Omega_glist(Zlist = zl_s,scale = scale_s, type = "homoscedastic")
zl_i = Zlist(f_i,df)
scale_i = scalelist(Zlist = zl_i,type="flat")
omega_glist_i = Omega_glist(Zlist = zl_i,scale = scale_i, type = "homoscedastic")
if(!is.null(f_si)){
zl_si = Zlist(f_si,df)
scale_si = scalelist(Zlist = zl_si,type="decreasing")
omega_glist_si = Omega_glist(Zlist = zl_si,scale = scale_i, type = "homoscedastic")
Omega = omega_glist_s$Omega + omega_glist_i$Omega + omega_glist_si$Omega+
Diagonal(n = nrow(df))*(max(scale_s,scale_i,scale_si)*1.5)^2}else{
Omega = omega_glist_s$Omega + omega_glist_i$Omega +
Diagonal(n = nrow(df))*(max(scale_s,scale_i)*1.5)^2}
err = MASS:::mvrnorm(n=1, mu= rep(0,NCOL(Omega)), Sigma=Omega)
df$y=err
#matrixcalc:::is.positive.definite(as.matrix(Omega))
df =permuco:::changeContrast(df,contr = contr.sum)
fqf=y ~ fS * fC * fI + Error(subject/(fI*fC)) + Error(item/(fS*fC))
lf= list.files(paste(dir,"R",sep=""))
for(lfi in lf){
print(lfi)
source(paste(dir,"R/",lfi,sep=""))
}
qf_p = aovperm(fqf, data = df, np = 4000,method = "terBraak",effect=1)
qf_p = aovperm(fqf, data = df, np = 4000,method = "terBraak_logp",effect=1)
anova_table_quasif(arg)
arg$mm
rankMatrix(z12)
profvis({
qf_p = aovperm(fqf, data = df, np = 2,method = "terBraak",effect=1)})
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