lshep
commented
6 years ago Hello,
Thank you for your interest in Bioconductor. Please see initial comments below:
BUILD REPORT
- [ ] Add unit tests
- [ ] Checking coding practice about sapply and 1:n structures
- [ ] Add runnable example to Parse.Rd
README
- [ ] I'm not exactly sure why you took this out but update to include Bioconductor installation instructions as originally had - you can include both github instructions and Bioconductor instructions.
VIGNETTE/CODING:
- [ ] clarification question - can there be infiniate number of samples? In your example data you show 2 - can this be any number?
- [ ] Vignette and sample code should also use coding practice advice of build report
- [ ] For future reference there does exists AtomicList structures in IRanges, like IntegerList or NumericList for lists of a consistent type
- [ ] It might be nice to have a specific show method and accessors for the "most important" or each value of output (ie. nllh(fits) would give the nllh output)
- [ ] Density, distribution, and quantile functions, plus simulating data section: you said you have to specify each modle parameter but it looks like you use default arguments from running your functions - and the original vector is stored in your function output so realistically couldn't the argument to qdiscgammagpd be 'fits' with a designated sample - if the user specifies an argument than use specified argument but else calculate based on default from 'fits'
- [ ] Doing comparative analysis section: The code in this section again appears like it could be better hidden within a function and the user only need to specifiy the object, then a selection of defaults could be used to do the calculation. It seems like distance, grid calucation and argument defaults all could be within this wrapper function.
NOTE I'm not going to insist on this, given that a class designed for this seems slightly overkill and its reuse would be unlikely, but for future reference you may consider designing packages with a designated class structure (S4 class) for output and input to other functions/methods (reusing any Bioconductor infastructure is most ideal). This is a more formalized way to define output/input and we strongly suggest it. This also allows for easier customized accessor methods, show methods, etc .... Given that the output is more list like and variable with statistical output, again I won't insist on it but just something to keep in mind for future Bioconductor submissions.
Please address the above issues and/or comment with clarification or justification. When you are ready for another review ensure that a new build is generated with a version bump and comment back here in some way addressing the above concerns for a second review. Thank you.
Cheers.
bioc-issue-bot
hillarykoch
mtmorgan
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