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# Sample R code for "PBSadmb" with the example "vonb.tpl"
# Before sourcing this file, have a valid file pathfile
# in the current working directory (default = "ADpaths.txt",
# but user can specify any file name in setupAD() ).
# Load R packages; ignore the GUI for now.
require(PBSmodelling); require(PBSadmb)
setupAD()
# Make and run "vonb.exe"
makeAD("vonb"); runAD("vonb");
# Read and unpack the report;
# i.e., create R variables with the same names used in "vonb.tpl"
vonb <- readList("vonb.rep"); unpackList(vonb);
# Plot the data
plot(age,y,pch=20,cex=2,col="blue",xlab="Age",ylab="Length (mm)");
lines(age,ypred,col="red",lwd=3);
# Check the calculations in R
ypredR <- Linf*(1-exp(-K*(age-t0)));
nobs <- length(age);
fvalR <- nobs*log(sigma) + sum((ypredR-y)^2)/(2.0*sigma^2)
cat("Functions values (ADMB & R):\n");
cat(fval," ",fvalR,"\n")
cat("Predictions (ADMB & R):\n");
cat(ypred,"\n");
cat(ypredR,"\n");
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