I managed to solve the problem myself using:

q=sort(unique(foram$stage[which(foram$length>0)]))


boxplot(foram$logl~foram$stage, data=foram, outline=F, at=q, axes=TRUE,
add=TRUE, col="gray82", medlwd=1)

points(foram$stage,foram$logl, cex=.1)


However, for future reference since this was my first post and I was trying
to give code like you requested, what did I do wrong? 
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