##############################################
#  Example Code for SPAr
##############################################


install.packages('SPAr', repos='http://cran.r-project.org',type="source")
library(SPAr)

data(SPA_example)
attach(SPA_example)

## compute p-values of dichotomous traits

pstar_dich <- SPA.I(x,y.d,nperm=100) #compute I1,I2 and p* and their p-values
print(pstar_dich)

I1_dich <- SPA.I(x,y.d,interaction=1,nperm=100) # only compute I1 and its pvalue
print(I1_dich)


## compute p-values of continuous traits

pstar_cont <- SPA.I(x,y.c,nperm=10,type="cont")  #compute I1,I2 and p* and their p-values
print(pstar_cont)

I1_cont <- SPA.I(x,y.c,type="cont",interaction=1,nperm=100) # only compute I1 and its pvalue
print(I1_cont)


## compute G-E interaction effect

SPA.I.GE <- SPA.I.GE(x,y.d,E,nperm=100)
print(SPA.I.GE)