extinction in nemoage

[Camilla Stefanini]

Hi everyone!

I was looking for a way to clear some specific patches at the end of a burnin simulation, and I thought about using the Extinction LCE with an extinction_rate matrix. However, it looks like extinction is not implemented in Nemoage version - is that correct?

>>>> WARNING:: Orphan parameters!
>>>> The following parameters do not belong to any simulation component:
>>>> "extinction"
>>>> "extinction_rate"

If yes, anybody would have a suggestion on how to clear specific patches at the end of a simulation?

Thank you!

Camilla

[Olivier Cotto]

Hi Camilla, 

Could you share the init file ? 

Olivier

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[Camilla Stefanini]

Dear Olivier, 

attached the init

thank you 

Camilla

[Frederic Guillaume]

Hi Camilla,

Unfortunately, the patch extinction LCE has not been ported to nemo-age yet. The alternative would be to set the carrying capacity to zero at a given generation to remove all individuals in a given patch at that generation. Not great when you have many patches, and you would have to specify all patch sizes at that generation. It would be better done with patch sizes stored in an external file.

I add a mental note that we need to add LCE extinction to nemo-age!

All the best,
Fred

[Camilla Stefanini]

Thank you Fred!

So if I want to remove some individuals from specific patches to simulated harvesting at the end of the burnin simulation, let's imagine at generation 50, I could simply set 

patch_nbfem (@g0 200, @g50  &matrix_with_some_0_patches.txt)

with 200 just a homogeneous initial value across all patches, to clear the patches where I want to cut individuals?

Then the actual simulation, where I input the source bin file, I could have some cleared patches where the harvesting occurred - correct?

Thank you very much, 

Camilla

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[Frederic Guillaume]

Hi,

Yes, that's correct! Note that the patches will be cleared after the regulation LCE and only if you use the "regulation_carrying_capacity" option (as you do).

Example:

## POPULATION

patch_number  625

patch_nbfem   (@g0 200, @g50  &matrix_with_some_0_patches.txt)

patch_nbmal   0

## LIFE CYCLE

breed_disperse 1

...

regulation     3

...

regulation_carrying_capacity

Make sure that no LCE brings additional individuals in the patches after the regulation LCE (eg, by dispersal, which isn't the case in your example).

Best

F.

[Camilla Stefanini]

Thank you very much Fred, 

just one last question - if I want to simulate different biological replicates with different and quite specific "clearing" schemes, and therefore different matrices_cutting.txt, is it possible to tell nemo to take one different file per replicate? so that each replicate is actually running with a replicate of these external matrices (N replicates = N clearing matrices we create = N nemo replicates) . It seems not by looking at the manual, but I just want to make sure. Otherwise the N replicates = Nclearing matrices we create x N nemo replicates, or we just have to use one precise cutting scheme for all Nemo replicates. 

Thank you very much!

Camilla

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[Frederic Guillaume]

Hi Camilla,

Yes, you can do this kind of replicate-specific parameterization in Nemo. You just need to pass multiple values to the "replicates" parameter, making it a sequential parameter. Here is how you'd do it:

replicates  1 1 1 1 1 1 1 1 1 1  # this will cause Nemo to run 10 different simulations, each with 1 replicate

You can do the same with a macro:

replicates rep(1, 10, sep=" ") # makes sure the values are separated by a white space and not a semi-colon with sep=" "

Then, setup your simulation parameters with a replacement string to insert the replicate number (= positional number of the simulation in the sequence of simulations)

replicates   rep(1, 10, sep=" ")  # sequential parameter %1

filename     mySim_r%'+'1

patch_nbfem  (@g0 200, @g50 &matrix_r%'+'1.txt)

That's it!

You would then also need to prepare 10 files named matrix_r1.txt to matrix_r10.txt.

I hope this helps,

Fred

[Frederic Guillaume]

err I made a mistake! sorry

The replacement string to include the replicate number in the file names is wrong, it should written like this: %'1[+]'1

The [+] indicates that the positional number is used and the 1 in front indicates the minimum number of digits use to write the number. Here "1" means we don't pad the number with "0" to the left.

F.