R/testLRT.r

In mvMORPH: Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data

################################################################################
##                                                                            ##
##                               mvMORPH: test.LRT                            ##
##                                                                            ##
##  Created by Julien Clavel - 02-02-2015                                     ##
##  (julien.clavel@hotmail.fr/ clavel@biologie.ens.fr)                        ##
##   require: phytools, ape, corpcor, spam                                    ##
##                                                                            ##
################################################################################

LRT<-function(model1, model2, echo=TRUE, ...){

## Options (TODO)
args <- list(...)
if(is.null(args[["simulations"]])){ simulations <- TRUE }else{ simulations <- FALSE}

##-------------------LRT comparison of the models-----------------------------##

if(any(class(model1)[2]!=class(model2)[2])){warning("You are using an LR test which is probably not at its nominal level!! You should use simulations-based LRT instead")}

if(model1$param$nparam<=model2$param$nparam){
    mod1<-model1;mod2<-model2
    L2<-model1$LogLik
    L1<-model2$LogLik
    model1<-mod2;model2<-mod1
    warning("The order of the models has been changed for the comparison")
}else{
L1<-model1$LogLik
L2<-model2$LogLik
}
# Set names
if(class(model1)[2]=="mvmorph.bm"){
    model1$param$model<-if(model1$param$constraint=="equal"){
        paste(model1$param$model," equal variance/rates")
    }else if(model1$param$constraint=="shared"){
        paste(model1$param$model," shared eigenvectors")
    }else if(model1$param$constraint=="proportional"){
        paste(model1$param$model," proportional")
    }else if(model1$param$constraint=="correlation"){
        paste(model1$param$model," shared correlation")
    }else if(model1$param$constraint=="diagonal"){
        paste(model1$param$model," diagonal")
    }else if(model1$param$constraint=="variance"){
        paste(model1$param$model," shared variance")
    }else if(model1$param$constraint=="equaldiagonal"){
        paste(model1$param$model," equal diagonal")
    }else{model1$param$model}
}

if(class(model2)[2]=="mvmorph.bm"){
    model2$param$model<-if(model2$param$constraint=="equal"){
        paste(model2$param$model," equal variance/rates")
    }else if(model2$param$constraint=="shared"){
        paste(model2$param$model," shared eigenvectors")
    }else if(model2$param$constraint=="proportional"){
        paste(model2$param$model," proportional")
    }else if(model2$param$constraint=="correlation"){
        paste(model2$param$model," shared correlation")
    }else if(model2$param$constraint=="diagonal"){
        paste(model2$param$model," diagonal")
    }else if(model2$param$constraint=="variance"){
        paste(model2$param$model," shared variance")
    }else if(model2$param$constraint=="equaldiagonal"){
        paste(model2$param$model," equal diagonal")
    }else{model2$param$model}
}

if(class(model1)[2]=="mvmorph.ou"){
    model1$param$model<-if(model1$param$decomp=="diagonal"){
        paste(model1$param$model," diagonal")
    }else if(model1$param$decomp=="equal"){
        paste(model1$param$model," equal")
    }else if(model1$param$decomp=="eigen"){
        paste(model1$param$model," symmetric")
    }else if(model1$param$decomp=="eigen+" | model1$param$decomp=="cholesky" | model1$param$decomp=="spherical"){
        paste(model1$param$model," symmetric positive")
    }else if(model1$param$decomp=="lower"){
        paste(model1$param$model," lower triangular")
    }else if(model1$param$decomp=="upper"){
        paste(model1$param$model," upper triangular")
    }else if(model1$param$decomp=="qr" | model1$param$decomp=="svd" | model1$param$decomp=="schur"){
        paste(model1$param$model," non-symmetric")
    }else if(model1$param$decomp=="qr+" | model1$param$decomp=="svd+" | model1$param$decomp=="schur+"){
        paste(model1$param$model," non-symmetric positive")
    }else{model1$param$model}
}

if(class(model2)[2]=="mvmorph.ou"){
    model2$param$model<-if(model2$param$decomp=="diagonal"){
        paste(model2$param$model," diagonal")
    }else if(model2$param$decomp=="equal"){
        paste(model2$param$model," equal")
    }else if(model1$param$decomp=="eigen"){
        paste(model1$param$model," symmetric")
    }else if(model2$param$decomp=="eigen+" | model2$param$decomp=="cholesky" | model2$param$decomp=="spherical"){
        paste(model2$param$model," symmetric positive")
    }else if(model2$param$decomp=="lower"){
        paste(model2$param$model," lower triangular")
    }else if(model2$param$decomp=="upper"){
        paste(model2$param$model," upper triangular")
    }else if(model2$param$decomp=="qr" | model2$param$decomp=="svd" | model2$param$decomp=="schur"){
        paste(model2$param$model," non-symmetric")
    }else if(model2$param$decomp=="qr+" | model2$param$decomp=="svd+" | model2$param$decomp=="schur+"){
        paste(model2$param$model," non-symmetric positive")
    }else{model2$param$model}
    
}

#
LRT<-(2*((L1-L2)))
#difference in degrees of freedom
ddf<-model1$param$nparam-model2$param$nparam

LRT.prob<-pchisq(LRT,ddf,lower.tail=FALSE)

if(echo==TRUE){
    if(LRT.prob<0.001){signif<-c("***")}else if(LRT.prob<0.01){
        signif<-c("**") }else if(LRT.prob<0.05){signif<-c("*")}else if(LRT.prob<0.1){signif<-c(".")}else{signif<-""}
    cat("-- Log-likelihood Ratio Test --","\n")
    cat("Model",model1$param$model," versus ",model2$param$model,"\n")
    cat("Number of degrees of freedom :",ddf,"\n")
    cat("LRT statistic:",LRT," p-value:",LRT.prob,signif,"\n")
    cat("---","\n")
    cat("Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1")
}

results<-list(pval=LRT.prob, ratio=LRT, ddf=ddf, model1=model1$param$model, model2=model2$param$model)
class(results)<-c("mvmorph.lrt")
invisible(results)
#End
}