Estimate of Sigma (2,1) is displayed as 0 in model when it shouldn't be displayed about bbr

[seth127]

@adamlafontaine can you run bbi nonmem summary [ctl file path] --json on the command line and paste in the output (or ideally just this parameter part of the output if you can easily extract it)?

If this is in that json that comes from bbi too then this should be an issue in https://github.com/metrumresearchgroup/babylon not here. I think that's probably the case, but I'm not sure.

[adamlafontaine]

It looks like it is in the json so I will create an issue for babylon then.

    "parameters_data": [
            {
                    "method": "TABLE NO.     1: First Order Conditional Estimation with Interaction: Goal Function=MINIMUM VALUE OF OBJECTIVE FUNCTION: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0",
                    "estimates": {
                            "theta": [
                                    0.432605,
                                    4.11838,
                                    1.11544,
                                    4.20827,
                                    1.2875
                            ],
                            "omega": [
                                    0.220155,
                                    0.0688803,
                                    0.0827208,
                                    0.13387,
                                    0.0735232,
                                    0.169307
                            ],
                            "sigma": [
                                    0.0397749,
                                    0,
                                    0.841006
                            ]
                    },
                    "std_err": {
                            "theta": [
                                    0.0630859,
                                    0.0276778,
                                    0.0328263,
                                    0.0191263,
                                    0.035593
                            ],
                            "omega": [
                                    0.0529672,
                                    0.0199708,
                                    0.00982676,
                                    0.0236165,
                                    0.0105625,
                                    0.0197401
                            ],
                            "sigma": [
                                    0.00125788,
                                    10000000000,
                                    2.87706
                            ]
                    },
                    "random_effect_sd": {
                            "omega": [
                                    0.469207,
                                    0.510415,
                                    0.287612,
                                    0.693395,
                                    0.621269,
                                    0.411469
                            ],
                            "sigma": [
                                    0.199436,
                                    0,
                                    0.917064
                            ]
                    },
                    "random_effect_sdse": {
                            "omega": [
                                    0.0564434,
                                    0.0975455,
                                    0.0170833,
                                    0.0689339,
                                    0.0524938,
                                    0.0239873
                            ],
                            "sigma": [
                                    0.00315357,
                                    10000000000,
                                    1.56862
                            ]
                    },
                    "fixed": {
                            "theta": [
                                    0,
                                    0,
                                    0,
                                    0,
                                    0
                            ],
                            "omega": [
                                    0,
                                    0,
                                    0,
                                    0,
                                    0,
                                    0
                            ],
                            "sigma": [
                                    0,
                                    1,
                                    0
                            ]
                    }
            }
    ],

[seth127]

I'm pretty sure we decided this is correct behavior and the user can filter these out if they want to. Also, with the new param_labels() function it will be easier to filter down to only the params that are actually specified in the control stream (aka not sigma(2,1)). See the vignette for an example:
https://metrumresearchgroup.github.io/rbabylon/articles/parameter-labels.html