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flr / FLXSA

The FLXSA package
http://flr-project.org/FLXSA
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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 #8

Open olfabenabdallah opened 3 years ago

olfabenabdallah commented 3 years ago

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

iagomosqueira commented 3 years ago

Could I get access to the input stock and indices objects?

olfabenabdallah commented 3 years ago

Could I get access to the input stock and indices objects?

Sorry for the delay replying to you, but I was in a sea trip.

I've attached the data you requested. DATA_XSA.zip

olfabenabdallah commented 3 years ago

@iagomosqueira Sorry for the delay replying to you, but I was in a sea trip.

I've attached the data you requested. DATA_XSA.zip

iagomosqueira commented 3 years ago

There was some information missing for FLXSA to work. discards.n and discards.wt needs to be specified, as 0 if that is the case, and then catch.n and catch.wt updated. Also, the plusgroup needs to be set to match what FLXSA assumes, last age

Please check if 0 and 4 are OK as minimum and maximum ages for fbar(). The ages considered to be fully selected should be used there. The example below sets them to 1 and 3, just as example.

This code runs here, could you please check and let us know?

Obviously the time series is pretty short, so results should be interpreted with caution. You could consider taking a look at FLa4a as a statistical model that can tell you quite a bit more about the quality of the fit and the information the data is really giving.

library(FLXSA)

stk <- readFLStock('DATA_XSA/MUT1214_1.IND')

# SET discards to zero
discards.n(stk) <- 0
discards.wt(stk) <- landings.wt(stk)

# COMPUTE catch
catch(stk) <- computeCatch(stk, "all")

# SET plusgroup
range(stk, 'plusgroup') <- 4

# CHECK minfbar and maxfbar, 0-4 is OK?
range(stk)

# CHANGE if needed, for example
range(stk, c('minfbar', 'maxfbar')) <- c(1, 3)

idx <- readFLIndex('DAT_XSA/MUTTUNEFF1.DAT')

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(stk, idx, FLXSA.control.aa)

library(ggplotFL)

plot(aa.xsa + stk)
olfabenabdallah commented 3 years ago

@iagomosqueira I can't express my gratitude for your help.

I tried considering your advices, however I get this error

aa.xsa <- FLXSA(stk, 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

iagomosqueira commented 3 years ago

I do not get that error. Could you please check what version of R, FLCore and FLXSA are you running?

R.version
packageVersion('FLCore')
packageVersion('FLXSA')

Did you install from the FLR repository?

olfabenabdallah commented 3 years ago

platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 4
minor 0.2
year 2020
month 06
day 22
svn rev 78730
language R
version.string R version 4.0.2 (2020-06-22) nickname Taking Off Again

packageVersion('FLCore') [1] ‘2.6.15’ packageVersion('FLXSA') [1] ‘2.6.4’

And yes, I install it from repository

iagomosqueira commented 3 years ago

I am testing it now in R 4.0.3, on Windows 10 64 bit, packages re-installed from the FLR repository, and I do not get that error.

Can you please save the objects created in your session

save(stk, idx, file="aa.RData")

and post it here?

olfabenabdallah commented 3 years ago

@iagomosqueira DATA_XSA - Copy.zip

iagomosqueira commented 3 years ago

The files are not different. I have also tested it with R 4.0.2 and it works here.

Just to check things, does the FLXSA example run for you?

data(ple4)
data(ple4.indices)
res <- FLXSA(ple4, ple4.indices)
olfabenabdallah commented 3 years ago

@iagomosqueira

No

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

iagomosqueira commented 3 years ago

So nothing to do with your data then. What version of iterators do you have?

packageVersion('iterators')

What do you get if you call

iter

I think the call to iter inside an lapply is not dispatching correctly.

olfabenabdallah commented 3 years ago

packageVersion('iterators') [1] ‘1.0.13’

iter standardGeneric for "iter" defined from package "iterators"

function (obj, ...) standardGeneric("iter") <environment: 0x000001dc3501c818> Methods may be defined for arguments: obj Use showMethods("iter") for currently available ones.

iagomosqueira commented 3 years ago

At this point I can only think of the option of installing R 4.0.3, just to have a clean R installation, and then install only iterators from CRAN and FLXSA from FLR. Is that possible for you? Your 4.0.2 installation will remain untouched.

I am afraid it is very difficult for me to fix the problem when I cannot replicate it.

olfabenabdallah commented 3 years ago

@iagomosqueira

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

[Workspace loaded from C:/Users/olfab/OneDrive/Desktop/MUT_STOCK ASSESSMENT_2020/MUT_ASSESSMENT_2020/MUT_TUN_2020/.RData]

Loading required package: FLXSA Loading required package: FLCore Loading required package: lattice Loading required package: iterators FLCore (Version 2.6.15, packaged: 2020-05-26 19:36:47 UTC) Loading required package: FLAssess

Restarting R session...

install.packages("iterators") Installing package into ‘C:/Users/olfab/OneDrive/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/iterators_1.0.13.zip' Content type 'application/zip' length 343160 bytes (335 KB) downloaded 335 KB

package ‘iterators’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\olfab\AppData\Local\Temp\Rtmpe2eGKX\downloaded_packages

install.packages("FLXSA", repos="http://flr-project.org/R") Installing package into ‘C:/Users/olfab/OneDrive/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) trying URL 'http://flr-project.org/R/bin/windows/contrib/4.0/FLXSA_2.6.4.zip' Content type 'application/zip' length 440017 bytes (429 KB) downloaded 429 KB

package ‘FLXSA’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\olfab\AppData\Local\Temp\Rtmpe2eGKX\downloaded_packages

setwd("C:/Users/olfab/OneDrive/Desktop/MUT_STOCK ASSESSMENT_2020/MUT_ASSESSMENT_2020/MUT_TUN_2020/RUN_BENCHMARK/DATA_XSA") library(FLXSA) Loading required package: FLCore Loading required package: lattice Loading required package: iterators FLCore (Version 2.6.15, packaged: 2020-05-26 19:36:47 UTC) Loading required package: FLAssess stk <- readFLStock('MUT1214_1.IND') discards.n(stk) <- 0 discards.wt(stk) <- landings.wt(stk) catch(stk) <- computeCatch(stk, "all") range(stk, 'plusgroup') <- 4 range(stk) min max plusgroup minyear maxyear minfbar maxfbar 0 4 4 2010 2019 0 4 range(stk, c('minfbar', 'maxfbar')) <- c(1, 4) idx <- readFLIndex('MUTTUNEFF1.DAT') 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(stk, 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

iagomosqueira commented 3 years ago

We will need to debug it in your machine, and see where the errror is coming from. If you call

 trace("FLXSA", browser, exit=browser, signature = c("FLStock", "FLIndices"))

and then

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

you will be going line by line inside the FLXSA method. Can you keep pressing enter until you get an error message and let me know in what line it stops?

iagomosqueira commented 3 years ago

This bug is due to the negative interaction between FLXSA's C++ code and RStudio and only in Windows we saw in #6. Quick solution is to run the code in plain R. Not sure there will be resources available to fix this, given than XSA has very limited use and it affects a single use case.

olfabenabdallah commented 2 years ago

Dear IagoI am returning to you because I had a problem when runing XSA on MUT I get an error after runing this command: aa.stk <- readFLStock("MUT1214_1.ind", no.discards=TRUE) Error in readVPA(file, quiet = quiet, sep = sep, na.strings = na.strings) :

This bug is due to the negative interaction between FLXSA's C++ code and RStudio and only in Windows we saw in #6. Quick solution is to run the code in plain R. Not sure there will be resources available to fix this, given than XSA has very limited use and it affects a single use case.

iagomosqueira commented 2 years ago

Could you please show what is the error message that readVPA returns?

olfabenabdallah commented 2 years ago

Could you please show what is the error message that readVPA returns?

Error in readVPA(file, quiet = quiet, sep = sep, na.strings = na.strings) :

iagomosqueira commented 2 years ago

Could you please share the VPA files? Either here or by email

olfabenabdallah commented 2 years ago

Could you please share the VPA files? Either here or by email @iagomosqueira DATA_XSA.zip

iagomosqueira commented 2 years ago

What version of R and FLCore do you have? This works for me here, R 4.12 and FLCore 2.6.18

library(FLCore)

stk <- readFLStock("DATA_XSA/MUT1214_1.IND")

discards.n(stk) <- 0
discards.wt(stk) <- landings.wt(stk)

catch(stk) <- computeCatch(stk, "all")

ind <- readFLIndex("DATA_XSA/MUTTUNEFF1.dat")
olfabenabdallah commented 2 years ago

What version of R and FLCore do you have? This works for me here, R 4.12 and FLCore 2.6.18

library(FLCore)

stk <- readFLStock("DATA_XSA/MUT1214_1.IND")

discards.n(stk) <- 0
discards.wt(stk) <- landings.wt(stk)

catch(stk) <- computeCatch(stk, "all")

ind <- readFLIndex("DATA_XSA/MUTTUNEFF1.dat")

@iagomosqueira R version: 4.0.3 FLCore version: 2.6.15

iagomosqueira commented 2 years ago

I have test it with R 4.0.5 and FLCore 2.6.16, the closest I have to your setup, and it works fine. readFLStock has not changed for a long time. Can you call

traceback()

after the error and post the output?

olfabenabdallah commented 2 years ago

@iagomosqueira

aa.stk <- readFLStock("MUT1214_1.ind", no.discards=TRUE) Error in readVPA(file, quiet = quiet, sep = sep, na.strings = na.strings) :

traceback() 3: stop() 2: readVPA(file, quiet = quiet, sep = sep, na.strings = na.strings) 1: readFLStock("MUT1214_1.ind", no.discards = TRUE)

iagomosqueira commented 2 years ago

Are you running this in Windows? And from RStudio?

olfabenabdallah commented 2 years ago

Are you running this in Windows? And from RStudio?

@iagomosqueira in windows but from R and not from RStudio

olfabenabdallah commented 2 years ago

Are you running this in Windows? And from RStudio?

@iagomosqueira in windows but from R and not from RStudio

@iagomosqueira Tried after installing the packages and got the same error tk <- readFLStock("DATA_XSA/MUT1214_1.IND") Error in readVPA(file, quiet = quiet, sep = sep, na.strings = na.strings) :

Henning-Winker commented 3 months ago

@iagomosqueira

No

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

Hi Olfa and Iago, I have done some checking with browser(), because I am having the same issue on my windows machine. So far, I am getting FLXSA to run when I set diag.flag=FALSE

test <- FLXSA(ple4, ple4.indices,diag.flag=FALSE)

So getting closer where to look.

iagomosqueira commented 2 months ago

The test above runs on windows with either diag.flag=TRUE or FALSE with the latest version of FLCore from R-Universe, 2.6.20.9100. Could you confirm @Henning-Winker what version do you have?