r-glmmextra: Extra methods for LMM methods

library(lme4)
#library(nlme)
m<-250
reps.n1<-2
reps.n2<-2

# grupos grandes
x2.g<-rnorm(m)
e2.g<-rnorm(m)
gg2<-gl(m,reps.n1*reps.n2)

x2.g.i<-x2.g[gg2]
b2<-x2.g.i+e2.g[gg2] # varianza teorica de b2->2



# grupos pequeños
x.g<-rnorm(m*reps.n1)
e.g<-rnorm(m*reps.n1)
gg<-gl(m*reps.n1,reps.n2)
x.g.i<-x.g[gg]
b<- x.g.i+e.g[gg] # varianza teorica de b->2


x.i<-rnorm(m*reps.n1*reps.n2)
e.i<-rnorm(m*reps.n1*reps.n2) # varianza del residuo -> 1
y<-b+b2+x.i+e.i

m.null<-lmer(y~(1|gg2/gg)) # varianza de b=2, varianza del residuo=2
m.full<-lmer(y~(1+x.i|gg2/gg)+x.g.i+x.i) # varianza de b=1, residuo=1 -> predigo a nivel global y local
#m.null.lme<-lme(fixed=y~1,random=~1|gg2/gg)
#m.full.lme<-lme(fixed=y~1+x.g.i+x.i,random=~1+x.i|gg2/gg)


lmmR2.0<-lmmR2(m.null,m.null)

lmmR2.1<-lmmR2(m.null,m.full)
#lmmR2.2<-lmmR2(m.null.lme,m.full.lme)

#print(summary(lmmR2.2))

test_that("Report correct values for lmer comparing null model with itself", {
	expect_equal(lmmR2.0$rb.r2.1, expected=0,tolerance=0.15,scale=1)
	expect_equal(lmmR2.0$rb.r2.2, expected=0,tolerance=0.15,scale=1)
	expect_equal(lmmR2.0$sb.r2.1, expected=0,tolerance=0.15,scale=1)
	expect_equal(lmmR2.0$sb.r2.2, expected=0,tolerance=0.15,scale=1)

#	r2.1=rb.r2.1, rb.r2.2=rb.r2.2, sb.r2.1=sb.r2.1, sb.r2.2=sb.r2.2
	
})


test_that("Report correct values for lmer comparing both models", {
	expect_equal(lmmR2.1$rb.r2.1, expected=0.50,tolerance=0.15,scale=1)
	expect_equal(lmmR2.1$rb.r2.2, expected=0.30,tolerance=0.15,scale=1)
	expect_equal(lmmR2.1$sb.r2.1, expected=0.30,tolerance=0.15,scale=1)
	expect_equal(lmmR2.1$sb.r2.2, expected=0.25,tolerance=0.15,scale=1)

#	r2.1=rb.r2.1, rb.r2.2=rb.r2.2, sb.r2.1=sb.r2.1, sb.r2.2=sb.r2.2
	
})

#test_that("Report similar values for nlme", {
#	expect_equal(lmmR2.1$rb.r2.1, lmmR2.2$rb.r2.1,tolerance=0.05)
#	expect_equal(lmmR2.1$rb.r2.2, lmmR2.2$rb.r2.2,tolerance=0.05)
#	expect_equal(lmmR2.1$sb.r2.1, lmmR2.2$sb.r2.1,tolerance=0.05)
#	expect_equal(lmmR2.1$sb.r2.2, lmmR2.2$sbs.r2.1,tolerance=0.05)

#	r2.1=rb.r2.1, rb.r2.2=rb.r2.2, sb.r2.1=sb.r2.1, sb.r2.2=sb.r2.2
	
#})

#m.null.lme<-lme(fixed=y~1,random=~1|gg2/gg)
#m.full.lme<-lme(fixed=y~1+x.g.i+x.i,random=~1+x.i|gg2/gg)


#Testing entropy function
#expect_that(entropy(c(1,1,2,2)),equals(1))
# NA omited from results
#expect_that(entropy(c(1,1,2,2,NA)),equals(1))
#expect_that(entropy(c(1,1,1,1)),equals(0))
#
#expect_that(entropy(c(1,1,1,1,NA)),equals(0))