documentation review checklist

Docs review checklist:

[x] createPredModel
[x] getFinalState
[ ] getSumStats
- this definitely needs an example. [JACOB - done]
- also need to list out the potential functions under @ param funs [JACOB - done]
- Also- is there a case where argument names are the same between functions and the list of named arguments in @ param moreArgs gets confused? [JACOB - this is a good question for Andy who wrote the function]
- is there an option to leave funs blank and return the defaults? If so, should make this apparent [JACOB - done]
[ ] runRole
- is there documentation on what "step information" is? Or we could put it here [JACOB - removed print param entirely for now, I don't think it should not be user facing]
[x] prepRebuild
[x] quickModel
[x] roleData-divStats
[ ] roleData-rawStats
- what is the difference between rawSpAbundance and rawAbundance? Needs clarification [JACOB - added what I think this is supposed to do, but another question for Andy]
[ ] roleData
- the details section needs a quick description of how to obtain the localComm, metaComm and rolePhylo objects [JACOB - done]
[] roleExperiment-methods
[x] roleExperiment
- kinks in experimentMeta and example need to be worked out. This function's in flux. [JACOB - yep will discuss soon and I'll make an issue for this]
[x] roleModel
[ ] roleParams
- What is the significance of "Determines the length of individual-level data vectors" for the individuals_local param for the user? I'm assuming this means "Determines the length of raw individual-level trait, abundance, and genetic data vectors returned for simulations," but it's not 100% clear. [JACOB - replaced with your improved description]
- For speciation_local, "The new local species can be either from a birth in the local community or an immigration from the metacommunity." How is the speciation "mode" here determined? A short indicator would help. [JACOB - added, it is using the dispersal_prob param]
- Under speciation_meta, "The sum of speciation_meta and extinction_meta is the average lifetime of phylogeny branches, and the larger this value the less new individual traits will deviate." What are the new individual traits deviating from? The metacommunity mean? The parental/immediate ancestral value? [JACOB - done]
- comp_sigma needs more detail. What does Selectivity of competition mean? [JACOB - added, but all of these are worth running by Andy or Isaac to maximize clarity and accuracy!]
- Is the mutation_rate per generation or per timestep? I'm assuming per generation, but best to be specific. [JACOB- I also think it is per gen, but will make sure]
- it looks like roleParams is defined twice in the script. I didn't change it out of fear that I break something, but it looks like a merge conflict gone wrong or something [JACOB- fixed!]
- I'm assuming that untbParams and lvParams are still in active development, so I'll refrain from adding anything for them. Might be good to have a short description for anyone testing them though. [JACOB- done for untb]
[ ] rolePhylo
- It looks like the params are repeated without documentation below the setClass() call. Is this intentional? [JACOB- oh yup the same kind of thing is in roleParams, I am unsure how/if arguments should be documented in relation to slots without repeating things]
[ ] setExpMetadata
- I added parameter descriptions and a @ details section based on what I think is going on. May need more detail and a look-over [JACOB- yup this is another one in flux in relation to auxMeta vs experimentMeta issue]
[x] simSeqs
- I'm assuming that this is internal or is under active development [JACOB - yup, moved to inst]
[x] writeRoLE
[ ] #51

Docs review notes: Each function needs a detailed Value section so users know what to expect the function to return. An example for most user-facing functions would be useful too. [JACOB - by value do you mean "return"? As of now they should all have returns but maybe could be more detailed. Also added preliminary examples]

role-model / roleR

documentation review checklist #49