Example for generating data returns Error

[jtdeweber]

I installed LIME today on R 4.1.3 after installing RTools, TMBhelper as directed. When attempting to follow the vignette example in "LIME: An R package for simulation and estimation using length data to account for variable fishing mortality and recruitment", I get the following error shown below. Apparently I do have the latest versions installed.

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

library(LIME)
lh <- create_lh_list(vbk=0.21,

•                  linf=65,
  

•                  t0=-0.01,
  

•                  lwa=0.0245,
  

•                  lwb=2.79,
  

•                  M=0.27,
  

•                  M50=34,
  

•                  M95=NULL,
  

•                  maturity_input="length",
  

•                  S50=20,
  

•                  S95=26,
  

•                  selex_input="length",
  

•                  binwidth=1,
  

•                  CVlen=0.1,
  

•                  SigmaR=0.737,
  

•                  SigmaF=0.2,
  

•                  R0=1,
  

•                  rho=0.43,
  

•                  nseasons=1)
  

true <- generate_data(modpath=NULL,

•                   itervec=1,
  

•                   lh=lh,
  

•                   Fdynamics="Ramp",
  

•                   Rdynamics="AR",
  

•                   Nyears=20,
  

•                   Nyears_comp=20,
  

•                   comp_sample=200,
  

•                   init_depl=0.8,
  

•                   seed=1)
  

Error in FUN(X[[i]], ...) : object 'R_t' not found

devtools::install_github("kaskr/TMB_contrib_R/TMBhelper")
Skipping install of 'TMBhelper' from a github remote, the SHA1 (d275e522) has not changed since last install.
Use force = TRUE to force installation
devtools::install_github("merrillrudd/LIME", build_vignettes=TRUE)
Skipping install of 'LIME' from a github remote, the SHA1 (9dcfc7f) has not changed since last install.
Use force = TRUE to force installation

Thank you for the help,

Tyrell DeWeber

[jtdeweber]

The error above was acquired when running the code from the PDF vignette - dated 2017.

When I run the script from Github directly, there is no error.

Thus, I suppose the issue is solved for me.

[xucamel]

@jtdeweber I have the same error, how did you solve it?

[jtdeweber]

there was apparently a problem with the PDF vignette. I ran the script from Github and had no error message then.

[Nuruyawild]

there was apparently a problem with the PDF vignette. I ran the script from Github and had no error message then.

How did you ran the script? I downloaded the zip file and install, but I also have the same error