initial values ignored

[jpritikin]

Describe the bug
Can't set initial values

To Reproduce
Run bug.tar.gz

Expected behavior
rawTwin[1] etc should be set to 0.5

Operating system
Linux Ubuntu 20.10

CmdStanR version number
0.1.3, using cmdstan-2.26.0

Additional context
Maybe a cmdstan bug?

[jpritikin]

Oops, you can comment tall[['ord']] <- ordinalize(tall[['value']], 12) and source("util.R") to get the script to run.

[mike-lawrence]

Check that you're structuring the inits properly. See this issue that boiled down to failure to do so.

[jpritikin]

Here's what I found in the init file:

{
  "predVar": 1,
  "eVar": 2,
  "rawFamily[1]": 0.5,
  "rawFamily[2]": 0.5,
  "rawFamily[3]": 0.5,
  "rawFamily[4]": 0.5,
  "rawFamily[5]": 0.5,
  "rawFamily[6]": 0.5,
  "rawFamily[7]": 0.5,
  "rawFamily[8]": 0.5,
  "rawTwin[1]": 0.5,
  "rawTwin[2]": 0.5,
  "rawTwin[3]": 0.5,
  "rawTwin[4]": 0.5,
  "rawTwin[5]": 0.5,
  "rawTwin[6]": 0.5,
  "rawTwin[7]": 0.5,
  "rawTwin[8]": 0.5
}

Check that you're structuring the inits properly

What can I do? It's cmdstanr that structures the output.

[jpritikin]

Oh, so I needed to do:

    initVal <- list(predVar=1, eVar=2)
    initVal[['rawFamily']] <- rep(.5, dl$numFamily)
    initVal[['rawTwin']] <- rep(.5, dl$numTwin)

Why doesn't cmdstanr prohibit square brackets in variable names?

[mike-lawrence]

Why doesn't cmdstanr prohibit square brackets in variable names?

Yup, that's what should happen. If you scroll to the bottom of the issue I linked, that's the solution that has been seemingly agreed-to as the solution to this. It just hasn't been implemented yet.

[rok-cesnovar]

In all honesty I forgot about that. Lets keep this issue here so we dont forget.