Some trouble shooting steps for plotting coexistence

[donahuem]

• when plotting within year dynamics every 10 years, add R to the plot of R so we know if there is no growth bc species enters after R= R for that species
• if this is the issue, make the R*s more similar or limit the amount of delay in germination - otherwise we will get lots of no coexistence runs But there are some other issues. Here is an example where species that are coexisting at y = t, are both extinct at y= t+10 It is possible that Species 1 goes extinct between the first and second plot (it was at ~1e-5 in the first figure) but I wouldn't think that Sp 2 would be extinct so quickly -- it was at 30 in the first figure. Why is this? Could be a problem in the extinction cut off - is it too low? Am I accidentally setting both species to be extinct instead of just one?

Also, would be nice to stop the run if both species go extinct to improve total run time.

[donahuem]

This happens again in the next run- one species goes extinct and the next one goes extinct a few years later.
This indicates to me that we need to limit the environment to a region where each species on its own will survive.

So, perhaps the first thing to do is define the parameter space where single species runs consistently survive, then we put both species in together. @dbuona this might be a good next step

[dbuona]

We thought the easiest way to make it a one species model was to immediately kill off species 2 (when I tried to set spp=1 it broke the code down the line). We did this by make N0<-c(100,0) which should mean there are 0 seeds in year 1 for species 2, but miraculously, in many runs, species 2 would still appear.