jg_extend: Extend JAGS model code

Description Usage Arguments Details Value

View source: R/extend.R


Extends JAGS model code, i.e., converts it from code in the JAGS dialect of the BUGS language to code in the JAGS dialect of the extended BUGS language. In addition to the data and model blocks the extended BUGS languge allows a predict and/or aggregate block. The predict block is used to estimate new expected values while the aggregate block is used to estimate metrics for the entire dataset. The former is useful for exploring the models predictions and calculation of residuals while the latter is useful for posterior predictive checking among other things. The advantages of separating the predictive and aggregative code from the model code are 1) the model code runs quicker; 2) the predictive code can be run with user provided datasets to generate predictions under unobserved combinations of data; 3) the predictive or aggregative code can be changed without requiring the model code to be rerun.





string of JAGS model code


In order for the current function to extend some JAGS code it requires the predictive and/or aggregative code segments to be identified line by line using a #' comment followed by one or more of the characters MPAmpa to indicate to which blocks the line of code belongs.

The syntax is as follows: the first line of code, i.e. model { is always #' M (it doesn't require setting) which indicates that it and all subsequent lines should only be included in the model block. This remains the case until the mode changes to for example #' MP which indicates that the current line and all subsequent lines should be included in the model and predictive blocks unless the mode changes again to for example #' A to indicate inclusion in the aggregative code block only. The only exception is if a line of code contains one or more of the lower case characters m, p and/or a. In this situation the mode is temporarily ignored and just the lower case characters are used to determine block inclusion for the current line only. It is worth noting that the block mode can be set and temporarily ignored in the same line. Thus #' Pm indicates change mode to predictive but only include the current line in the model block. The order of the characters doesn't matter but they must form the first word after #' which must be the first hash character on the line. Duplicates are ignored and a warning is issued for any characters other than MPAmpa - the extraneous characters are ignored.


String of model code in JAGS dialect of extended BUGS language or FALSE if fails (in which case also issues an error).

poissonconsulting/juggler documentation built on Sept. 7, 2017, 1:55 p.m.