R/readfit.r

In R2admb: 'ADMB' to R Interface Functions

## from Anders Nielsen
read.fit<-function(file){
#
# Function to read a basic AD Model Builder fit.
#
# Use for instance by:
#
#
## simple.fit <- read.fit('c:/admb/examples/simple')
#
# Then the object 'simple.fit' is a list containing sub-objects
# 'names', 'est', 'std', 'cor', and 'cov' for all model
# parameters and sdreport quantities.
#
  ret<-list()
  parfile<-as.numeric(scan(paste(file,'.par', sep=''),
                           what='', n=16, quiet=TRUE)[c(6,11,16)])
  ret$nopar<-as.integer(parfile[1])
  ret$nlogl<-parfile[2]
  ret$maxgrad<-parfile[3]
  file<-paste(file,'.cor', sep='')
  lin<-readLines(file)
  ret$npar<-length(lin)-2
  ret$logDetHess<-as.numeric(strsplit(lin[1], '=')[[1]][2])
  sublin<-lapply(strsplit(lin[1:ret$npar+2], ' '),function(x)x[x!=''])
  ret$names<-unlist(lapply(sublin,function(x)x[2]))
  ret$est<-as.numeric(unlist(lapply(sublin,function(x)x[3])))
  ret$std<-as.numeric(unlist(lapply(sublin,function(x)x[4])))
  ret$cor<-matrix(NA, ret$npar, ret$npar)
  corvec<-unlist(sapply(1:length(sublin), function(i)sublin[[i]][5:(4+i)]))
  ret$cor[upper.tri(ret$cor, diag=TRUE)]<-as.numeric(corvec)
  ret$cor[lower.tri(ret$cor)] <- t(ret$cor)[lower.tri(ret$cor)]
  ret$cov<-ret$cor*(ret$std%o%ret$std)
  return(ret)
}

## comparison of read.fit() and