Nothing
per.locus.like <-
function(a1, a2, locustype, r1, r2, s1, s2, h){
p <- h * r1 + (1 - h) * s1
q <- h * r2 + (1 - h) * s2
if(locustype== "C" | locustype=="c"){
if (length(r1)==0 | length(r2)==0 | length(s1)==0 | length(s2)==0){
return(NA)
}
else if(r1 == s1 && r2 == s2){
return(NA)
}
}
else if (locustype=="H" | locustype=="h" | locustype=="D" | locustype=="d"){
if (length(r1)==0 | length(s1)==0) return(NA)
else if (r1 == s1) return(NA)
}
if (locustype == "D" | locustype=="d"){
if (is.na(a1)==FALSE){
if(a1 == 1) { ## band present
return(log(p^2 + 2 * p * q))
}
else if (a1 == 0){ ## band absent
return(log(p^2)) ## r1 and s1 will be for the state that is observed
}
}
else return(NA)
}
else if (locustype == "H" | locustype== "h"){ ## haploid
return(log(p))
}
## if data are codominant
else if (is.na(a1)==FALSE & is.na(a2)==FALSE){
if(a1 == a2){
return(log(p^2))
}
else if (a1 != a2){
return(log(2 * p * q))
}
}
else {
return(NA)
}
}
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