VPA-tutorial: FLXSA- retrospective analyses

[JBLecomte]

Hello,

I am trying to reproduce the VPA tutorial for North Sea Plaice stock using FLXA:

After loading the data, I run the FLXSA function:

library(FLCore)
library(FLAssess)
library(FLXSA)
data(ple4)
data(ple4.indices)
xsa.control <- FLXSA.control()
ple4.xsa    <- FLXSA(ple4, ple4.indices, xsa.control)

and then I want to perform a retrospective analysis using:

retro.years <- 2012:2017 # updated values from online tutorial
ple4.retro <- tapply(retro.years, 1:length(retro.years), function(x){
  window(ple4,end=x)+FLXSA(window(ple4,end=x),ple4.indices)
})

I get the following error:
Error in lapply(assess@index, FLQuant) : negative length vectors are not allowed

It seems like I can't call 2 or more than 2 FLXSA in the same R session. Any idea, on how to perform a retrospective analysis using FLXSA ?

Thanks,

Here is my session info:

R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] FLXSA_2.6.3 FLAssess_2.6.3 FLCore_2.6.14 iterators_1.0.12 lattice_0.20-38
loaded via a namespace (and not attached):
[1] MASS_7.3-51.4 compiler_3.6.2 Matrix_1.2-18 tools_3.6.2 grid_3.6.2 stats4_3.6.2

[iagomosqueira]

I have tested the same code, with packages installed from the repository, and it runs without problems in both Linux and Windows 10.

Can you try using only lapply?

ple4.retro <- lapply(retro.years, function(x){
  window(ple4,end=x)+FLXSA(window(ple4,end=x),ple4.indices)
})

[JBLecomte]

Thanks for your answer, I was able to run all the code without error by using R directly. When I run the same code from RStudio I get the error, I mentioned above. I don't understand why Rstudio is causing the error, I will look into it tomorrow.

[JBLecomte]

I found the issue, the most recent RStudio version (1.2.5033) is causing the error, while the RStudio
version 1.1.463 is running fine. I will send the issue to Rstudio. Thanks for your help.

[iagomosqueira]

Thanks for letting us know. Is maybe one of packages loaded with RStudio redefining tapply in any way? Did it work in Rstudio using only lapply?

[JBLecomte]

With the last version of RStudio (1.2.5033) both lapply and tapply fail. I sent an issue on the rstudio repo this morning to let them know about this problem.