Here is a paper on Darwin's method, arguing that it was neither purely inductive nor deductive. Darwin worked on "hunches," or, as I would say, "informed hypotheses" based on previous research. His Notebooks, about which I have written before, show this.
The paper runs "into open doors," as it were, or argues for the obvious. It is also philosophically primitive. Of course, induction in a simple-minded Baconian sense does not work. Karl Popper argued quite a while ago about the non-existent method of "collecting facts and then 'drawing conclusions.'" Rather, he said, we formulate bold or not so bold theories as answers to questions that we can then test. One has to understand the "problem situation" (Collingwood) in which an author found herself or himself.
The notebooks are interesting, among other things, because they allow us to understand what Darwin at various stages thought was the problem to be solved.
1. See here, here, and here.