VPA does not compute stock.n for the whole series

[iagomosqueira]

If the example in VPA.Rd is run, abundances are only calculated back to 2003 for all ages, and then the cohort starts disappearing.

[marchtaylor]

I have just noticed that this example does not provide harvest values for the final year of the ple4 stock object (2008); rather "2001" was used - and the VPA fails. The following works:

# use the ple4 data set
data(ple4)
ple4.test <- ple4
# Remove 0s and set as 1s
catch.n(ple4.test)[catch.n(ple4.test)==0] <- 1
# Remove harvest and stock.n values
stock.n(ple4.test)[] <- NA
harvest(ple4.test)[] <- NA
# Set Fs in final year and final ages
harvest(ple4.test)[,"2008"] <- harvest(ple4)[,"2008"]
harvest(ple4.test)["10",] <- harvest(ple4)["10",]
# Run the VPA
ple4.vpa <- VPA(ple4.test)
# Take a look at the harvest
plot(harvest(ple4.vpa))