flr / flxsa

The FLXSA package

FLXSA

• Version: 2.6.5.9002
• Date: 03-05-2022
• Author: Laurence T. Kell
• Maintainer: FLR Team
• Repository: https://github.com/flr/FLXSA/
• Bug reports: https://github.com/flr/FLXSA/issues

Overview

FLXSA provides the framework to perform eXtended Survivor Analysis in FLR.

To install this package, start R and enter:

install.packages("FLXSA", repos="http://flr-project.org/R")

Documentation

• Help pages

Build Status

Releases

• All release

License

Copyright (c) 2004-2022 The FLR Team. Released under the GPL v2.

Contact

You are welcome to:

• Submit suggestions and bug-reports at: https://github.com/flr/FLXSA/issues
• Send a pull request on: https://github.com/flr/FLXSA/
• Compose a friendly e-mail to:

flxsa's Issues

q

Error in h(simpleError(msg, call)) : error in evaluating the argument 'X' in selecting a method for function 'lapply': negative length vectors are not allowed

Tried to run FLXSA function but getting error

FLXSA.control.aa <- FLXSA.control(x=NULL, tol=1e-09, maxit=30, min.nse=0.3, fse=0.5, rage=1, qage=3, shk.n=TRUE, shk.f=TRUE, shk.yrs=2, shk.ages=2,window=100, tsrange=20, tspower=3, vpa=FALSE)

aa.xsa <- FLXSA(aa.stk, aa.idx, FLXSA.control.aa)

Error in h(simpleError(msg, call)) :
error in evaluating the argument 'X' in selecting a method for function 'lapply': negative length vectors are not allowed

Error in SSB calculation

Hi!
I am currently trying to apply the XSA to one of ICES redfish stocks. I thought I followed the tutorial, however now the XSA values for SSB look rather unreasonable. So far I have uploaded my data, converted it to an FLStock object and defined the range, m, m.spwn and maturity at age. Afterwards I computed landings, discards and catch.

After running the XSA with a survey index and the default xsa.control, calculations for F and recruits seem reasonable, while SSB is given from 3.8 million to Inf.
I checked the input/output for stock.n, mat, and mean weight, seeing as these parameters are needed for the calculation, but they seem ok. The only parameter that is not calculated is ’stock’. I am not sure exactly why that is, or if it even is relevant for the calculation of SSB.

I’d be very grateful for any help on the matter!

Missing phenotype value

Hi, I would like to ask what to do if I have missing phenotype values? What does the phenotype file use to represent, is it NA or 0 or is it empty?

SE of q.hat reported incorrectly in diagnostics() function

the diagnostics function calculates the se of the log q as follows:

 S.E_Logq = round(c(sd(matrix([email protected][[f]], 
                  dim([email protected][[f]])[2], dim([email protected][[f]])[1], 
                  byrow = T), na.rm = T)), 4)

It therefore assumes the se is the same for all ages, when you look at the old VPA95 output, you get different se estimates for each age. You can replicate this by simply doing this:

apply([email protected][[f]],1,sd)

presumably this is a bug in the diagnostics function

XSA exception in Rstudio 1.2.xx version

Hello. If you try to perform typical XSA in new version FLXSA package with Rstudio 1.2.xx then you will got error:

Error in lapply(assess@index, FLQuant) : 
  negative length vectors are not allowed

You can simply reproduce this bug with test data (ple4):

data(ple4)
data(ple4.indices)
test <- FLXSA(ple4, ple4.indices)

Is there any solution exist or i should rollback to previous version? Problem occured only in Windows OS and Rstudio 1.2.xx or newst.

UPD: another members in comments found problem source in flxsa.R in fqs() function in lapply() calling from res <-fqs(.Call("runFLXSA", stock, indices, control, diag.flag))

Error in h(simpleError(msg, call)) : error in evaluating the argument 'data' in selecting a method for function 'bubbles': unable to find an inherited method for function ‘index.res’ for signature ‘"FLStock"’

Hi,

I tried to run a FLXSA but I had an error in the residuals function:

Model: xsa_control <- FLXSA.control(x=NULL, tol=1e-09, maxit=150, min.nse=0.3, fse=1.5,
rage=0, qage=2, shk.n=TRUE, shk.f=TRUE, shk.yrs=3, shk.ages=2,
window=100, tsrange=20, tspower=0, vpa=FALSE)

Log Residuals

ttl <- list(label="Log residuals for surveys for Parapenaeus longirostris in GSA 5", cex=1)
yttl <- list(label="log residuals", cex=0.8)
xttl <- list(cex=0.8)
stripttl <- list(cex=0.8)
ax <- list(cex=0.7)
par(mfrow=c(1,3))
bubbles(age~year, data=index.res(stk.xsa)[1,], bub.scale=5,
main=ttl, ylab=yttl, xlab=xttl, scales=ax, par.strip.text=stripttl)

And here it appears the error:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'data' in selecting a method for function 'bubbles': unable to find an inherited method for function ‘index.res’ for signature ‘"FLStock"’

Besides, for the same model I had another error in the "diagnostics" function using the FLEDA package:

diagnostics(stk.xsa)

And it appear the error: "Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘diagnostics’ for signature ‘"FLStock"’

Does anybody knows what can be happeing?

Thanks

Failed to install on Ubuntu

Hi,

I try to install FLXSA on Ubuntu:
/usr/lib/R/etc/Makeconf:168: recipe for target 'fl__vpa.o' failed
make: *** [fl__vpa.o] Error 1
ERROR: compilation failed for package ‘FLXSA’

• removing ‘/home/george/R/x86_64-pc-linux-gnu-library/3.4/FLXSA’
  Warning in install.packages :
  installation of package ‘/home/george/Downloads/FLXSA_2.5.tar.gz’ had non-zero exit status

Maybe do you have any idea.

Cheers !
George