fishnets/fishnets — pull request #15 by cttedwards (2014-08-18 02:14:18+00:00)
Title: Natural mortality nodes development

Have made various changes to the code during development of the natural mortality nodes. In particular I've included some modifications to the Brter() and Node() functions that could do with a check.

For Brter() I've tried to make the handling of NA values more explicit, with options to include or exclude predicted values according to whether covariate data are present to perform the prediction. This means that the predicted outputs can be made consistent with those from Glmer(). I've also include a predict.safe() function. This is intended for use in intermediary nodes within a fishnet, so that if some life-history data are present in a dataframe, they are not over-written when the fishnet is called during prediction. Finally there is a 'pars' option that allows finer control of which covariates in a formula are included during a model fit.

For Node() I have made changes to the Node$cross() function. First off I have amended the output results table to include observed and predicted (hat) values for the predictand. This means that plots of obs vs hat can be used to examine performance. There is now also a jacknife option which I've found useful for evaluation.