make_ipm() hangs when kernel_seq is specified

[Aariq]

I'm iterating a general stochastic kernel sampled IPM and it hangs when I specify kernel_seq. The vital rate models are GAMs with a random effect of year and in the IPM predict() is called with newdata = data.frame(year = yr) and par_set_indices = list(yr = 2000:2009). I tracked the hanging down to this line of .make_usr_seq():

https://github.com/levisc8/ipmr/blob/c40603ed76a53f58b7af09b2109823c9d826cf38/R/internal-make_ipm.R#L935

I don't understand why, but this call to grepl() is incredibly slow for my IPM. I don't quite understand what this line is doing or why it is so slow for my IPM but not noticeable for the one in the vignette. I assume there is a way to make this more efficient?

[Aariq]

Oh, the other problem with this line is that it's not looking through the unique values of kernel_seq. Shouldn't it be

  for(i in seq_along(unique(kernel_seq))) {

    nms_test[i] <- any(grepl(unique(kernel_seq)[i], pos_ids))

  }

?

[levisc8]

That is weird, I'll have to investigate that a bit more. How many iterations are you running it for?

[Aariq]

It completely hangs even with 10 iterations. It seems like grepl() doesn't need to look through the entire proto_ipm to figure out if the values in kernel_seq are reasonable.

[levisc8]

Yea, I just looked at the code you linked and it is definitely wrong. I'll get to that next week. Thanks for bringing this to my attention!

[Aariq]

Is there any reason this wouldn't do the trick?

  for(i in seq_along(unique(kernel_seq))) {

    nms_test[i] <- any(grepl(unique(kernel_seq)[i], unlist(pos_ids$par_set_indices)))

  }

I assume that would be faster.

[Aariq]

Or ditch the for-loop entirely?

if(! all(unique(kernel_seq) %in% unique(pos_ids$par_set_indices)) {
stop("not all values of 'kern_seq' are present in the kernel names.  Please check the model definition.")
}

[levisc8]

Should be fixed in development version now, and am submitting to CRAN as I need a slew of updates for Rpadrino anyway. I'd suggest waiting til I've done all testing before downloading and using this for "real work". Going to close now, but please feel free to re-open if you still have problems with it.