Clear error message in PBD::pbd_ML

[richelbilderbeek]

I have a hard time finding out how to use pbd_ML. I wish the error message would be more hulpful, to point a user into the right direction.

Say, I want to do a maximum likelihood optimization for the speciation completion rate. This is one of the many ways I've tried:

# Goal: optimize the SCR
branching_times <- c(1, 2, 3, 4)
erg <- 0.1 # Extinction Rate of Good species
eri <- 0.2 # Extinction Rate of Incipient species
scr <- 0.3 # Speciation Completion Rate
# ML assumes these are the same
sirg <- siri <- 0.4 # Speciation Initiation Rate of Good/Incipient Species

out <- PBD::pbd_ML(
  brts = branching_times,
  idparsopt = 3, # SCR
  initparsopt = scr,
  idparsfix = c(1, 2, 4),
  parsfix = c(sirg, erg, eri),
  exteq = TRUE,
  verbose = TRUE
)

The error message is:

The arguments should be coherent.

I wish the error message would be more detailed. Sure, I can look into the code (and I will in a sec), but it may be preferable to be more helpful to the user.

[rsetienne]

Hi Richel, exteq = TRUE is incompatible with having four parameters. exteq = TRUE means the extinction rates of good and incipient species are always the same, so no need to set it. A more informative error method would indeed be helpful... Cheers, Rampal

…

On 8-11-2018 13:46, Richel Bilderbeek wrote: I have a hard time finding out how to use |pbd_ML|. I wish the error message would be more hulpful, to point a user into the right direction. Say, I want to do a maximum likelihood optimization for the speciation completion rate. This is one of the many ways I've tried: |# Goal: optimize the SCR branching_times <- c(1, 2, 3, 4) erg <- 0.1 # Extinction Rate of Good species eri <- 0.2 # Extinction Rate of Incipient species scr <- 0.3 # Speciation Completion Rate # ML assumes these are the same sirg <- siri <- 0.4 # Speciation Initiation Rate of Good/Incipient Species out <- PBD::pbd_ML( brts = branching_times, idparsopt = 3, # SCR initparsopt = scr, idparsfix = c(1, 2, 4), parsfix = c(sirg, erg, eri), exteq = TRUE, verbose = TRUE ) | The error message is: |The arguments should be coherent. | I wish the error message would be more detailed. Sure, I can look into the code (and I will in a sec), but it may be preferable to be more helpful to the user. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#26>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ANkzmQFt-TIC7AeEroGO4DMQd5cOxPU-ks5utCeSgaJpZM4YUmxm>.

[richelbilderbeek]

Agree, that's one/a solution. This Issue is about helping other users get there faster.