diff --git a/R/ABneutral.R b/R/ABneutral.R index 96eac9a..dc5f925 100644 --- a/R/ABneutral.R +++ b/R/ABneutral.R @@ -105,8 +105,9 @@ ABneutral<-function(pedigree.data, p0uu, eqp, eqp.weight, Nstarts, out.dir, out. LSE_intercept<-function(param_int) { - sum((pedigree[,4] - param_int[4] - divergence(pedigree, p0mm, p0um, p0uu, param_int[1:3])[[2]])^2) + - eqp.weight*nrow(pedigree)*((divergence(pedigree, p0mm, p0um, p0uu, param_int[1:3])[[1]]- eqp)^2) + d = divergence(pedigree, p0mm, p0um, p0uu, param_int[1:3]) + sum((pedigree[,4] - param_int[4] - d[[2]])^2) + + eqp.weight*nrow(pedigree)*((d[[1]]- eqp)^2) } diff --git a/R/BOOTmodel.R b/R/BOOTmodel.R index 0d2445d..5363e2f 100644 --- a/R/BOOTmodel.R +++ b/R/BOOTmodel.R @@ -130,6 +130,7 @@ BOOTmodel<-function(pedigree.data, Nboot, out.dir, out.name) ## Defining the Least Square function to be minimized LSE_intercept<-function(param_int) { + d = divergence(pedigree, p0mm, p0um, p0uu, param_int[1:4]) sum((pedigree[,4] - param_int[5] - divergence(pedigree, p0mm, p0um, p0uu, param_int[1:4])[[2]])^2) + eqp.weight*nrow(pedigree)*((divergence(pedigree, p0mm, p0um, p0uu, param_int[1:4])[[1]]- eqp)^2) } @@ -158,7 +159,7 @@ BOOTmodel<-function(pedigree.data, Nboot, out.dir, out.name) counter<-counter+1 - message("Bootstrap interation: ", counter/Nboot, "\n") + message("Bootstrap interationsssss: ", counter/Nboot, "\n") opt.out <- suppressWarnings(optimx(par = param_int0, fn = LSE_intercept, method=optim.method)) alphafinal<-as.numeric(opt.out[1]) @@ -1000,8 +1001,9 @@ BOOTmodel<-function(pedigree.data, Nboot, out.dir, out.name) LSE_intercept<-function(param_int) { - sum((pedigree[,4] - param_int[4] - divergence(pedigree, p0mm, p0um, p0uu, param_int[1:3])[[2]])^2) + - eqp.weight*nrow(pedigree)*((divergence(pedigree, p0mm, p0um, p0uu, param_int[1:3])[[1]]- eqp)^2) + d = divergence(pedigree, p0mm, p0um, p0uu, param_int[1:3]) + sum((pedigree[,4] - param_int[4] - d[[2]])^2) + + eqp.weight*nrow(pedigree)*((d[[1]]- eqp)^2) } @@ -1028,7 +1030,7 @@ BOOTmodel<-function(pedigree.data, Nboot, out.dir, out.name) counter<-counter+1 - message("Bootstrap interation: ", counter/Nboot, "\n") + message("Bootstrap iterations: ", counter/Nboot, "\n") opt.out <- suppressWarnings(optimx(par = param_int0, fn = LSE_intercept, method=optim.method))