Migrating from earlier versions of rfishbase

[cboettig]

Many of the function calls and return types in rfishbase 0.* were relatively crude, and thus it does not make much sense to mimic them. Instead, we should simply provide a guide to users to map any functionality in the original version into the 2.0 version.

Here's a complete list of functions in the current (v0.2-3) NAMESPACE, along with mappings that exist so far. Will continue to update this as we get further along in rfishbase2.0.

• findSpecies, fish_names, which_fish(Family/Order/Class = x), getIds are all replaced by species_list()
• getDepth() is now in species_info() (see fields list)
• getEnviroClimateRange() basic information is in species_info(), more details in the various distribution functions and in ecology() table.
• getFaoArea() is now faoareas()
• getFoodItems is now fooditems()
• getLengthWeight() is now length_weight()
• getMetabolism is now oxygen()
• getPictures() pending ...
• getPredators() is now predators()
• getQuantTraits was a rather arbitrary combination of traits, now better allocated. Some of these are returned by the general species_info() table, others by specific tables such as morphology() or morphometrics()
• getRefs() pending
• getSize() is in species_info()
• getTrophicLevel is in ecology()
• loadCache and updateCache are no longer needed, all functions are live except for queries to the taxa-table, which still uses caching and has load_taxa(update=TRUE) to update the cache.
• which_fish() There are no longer generic methods to query for which species match certain criteria. The current approach requires querying the complete table wherein such data are held and filtering that. Some examples of this should be added to the vignette.

[fishandfish]

@cboettig , This is great work, keep it up. Cheers, K

[cboettig]

Available tables are given by heartbeat(). Working on API-level documentation that can return a more complete description of what is in each of these tables.