Code errors

[paulgovan]

This issue is for openjournals/joss-reviews#2111.

After taking a cursory review of the code, there seem to be problems with some of the functions. For example fit_analytic does not seem to be a recognized function. The code/documentation needs to be updated before a more in-depth review is possible.

Also, I would recommend a more description naming convention for the package. Functions like 'fit' and 'estimate' are very vague and can be confusing when working with multiple packages at the same time.

[donaldRwilliams]

fit_analytic is not a function in the package, so not really sure how to address this. If you are referring to the example in estimate.R, then fit_analytic is the name of an object--i.e.,

#' # analytic approach (sample by setting analytic = FALSE)
#' fit_analytic <- estimate(Y, analytic = TRUE)

Note also we do not have a function named fit. The function estimate estimates GGMs (and note changing names of functions would be quite the change considering the package is already on CRAN, researchers use it, etc.)

[paulgovan]

The examples in the README should be updated so that they are stand alone. For example, the fit_analytic object is not defined in the README, so these examples are not reproducible. I would also recommend checking the other documentation for similar issues.

[donaldRwilliams]

I see that now. I will fix it and check all the examples !

[jayrobwilliams]

Another option would be to include fit_analytic as a data object in the package, as bfi is currently. I'll also note that this issue is included in the paper as well as the README.

[donaldRwilliams]

Hi, yes, I fixed this.