getYield() error when using effort as an array

[jpwrobinson]

I've been playing around with mizer's North Sea multispecies model, particularly estimating yields under different fishing pressure. The getYield() function has been working fine for this (in many scripts since June, no problems), but now gives this error:

getYield(sim2)
      sp
time   Sprat Sandeel N.pout Herring Dab Whiting Sole Gurnard Plaice
      sp
time   Haddock Cod Saithe
Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
5: In sweep(f_gear, c(1, 3, 4), biomass, "*") :
  STATS is longer than the extent of 'dim(x)[MARGIN]'

The error now appears running the simple North Sea example at https://sizespectrum.org/mizer/articles/a_multispecies_model_of_the_north_sea.html. Using the NS_params in your data folder, I'm running:

# load species, gear params
load('data/NS_params.Rdata')

## get effort
f_location <- system.file("doc/NS_f_history.csv", package = "mizer")
f_history <- as(read.csv(f_location, row.names = 1), "matrix")
relative_effort<-f_history

# stick 100 years of initial fishing effort, set to 1957 levels
initial_effort <- matrix(relative_effort[1, ], byrow = TRUE, nrow = 100,
                         ncol = ncol(relative_effort), dimnames = list(1867:1966))
relative_effort <- rbind(initial_effort, relative_effort)

sim <- project(params, effort=relative_effort, dt=0.25)
getYield(sim)

getYield() works if you run the simulation with effort = 0. Could be a bug from a recent update on how effort is defined?

Thanks for all your work on this package, it's fantastic and easy to use.

[gustavdelius]

James, thank you very much for this useful bug report. The issue arises because the new code assumed that the dimensions of the effort array are called "time" and "gear", but the code does not ensure that these dimensions are named correctly. I have now fixed that. You can get the fixed version with

remotes::install_github("sizespectrum/mizer")

Alternatively, you can assign names to the effort array dimensions by hand:

names(dimnames(relative_effort)) <- c("time", "gear")

or, if you want to work with an existing simulation called sim then

names(dimnames(sim@effort)) <- c("time", "gear")

[jpwrobinson]

Incredible. Thanks for the super fast fix Gustav, much appreciated.