A number of small code refactors.

- Remove meaningless variable name 'value'
- Add method to SpeciesParam to specify a default value to avoid checking for NaNs over and over
- Add IntelliJ files, random.state, results and bin to gitignore
- Fix typos in documentation
- Add error message to ReactionFactor to improve debugging
Merge pull request #52 from fophillips/minor-refactors

A number of small code refactors