by gwhite » Wed Nov 27, 2019 7:19 pm
You are correct that lambda should have the log link function applied, with exp() the back transformation. The lambda parameter is one of several that the numerical code knows to use the log link with even though you have specified the logit link. Unfortunately, the plotting code isn't that smart.
So you can handle this in 2 different ways. First, if the problem is well-behaved, you could specify the log link as the default. The r parameter will be correctly estimated IF if isn't at the boundary of 1.
However, the second and preferred approach is to use the parameter-specific link function, specifying logit for r and log for lambda. You will get exactly the same model as if you has specified logit for all parameters, but now the plot package will know to use log/exp for the lambda parameter.
Gary