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I work from pages which I can turn rather than from PDFs, although I use PDFs to check for scope of a topic I may have earlier decided is not indexable, but later decided it is and I need to find all instances of it. I can either receive PDFs by email attachment or view them at an FTP site. I prefer to wait for the page proofs to arrive, but if it will speed things up, I can accept the PDFs and get them printed. I prefer working from at least the second set of page proofs. Sometimes too much reflows when working from first pages.
An indexable page is any page that must be read to determine if there's anything indexable on it. In general, front matter is not indexed - not the preface or forward, not the acknowledgements. Introductions are indexable if they add to the subject matter discussed in the book. Glossaries and bibliographies are usually not indexed. There can be circumstances where any of these parts of the book may be indexed.
Footnotes or endnotes may or may not be indexed. Some feel these are peripheral to the main argument of the book and don't belong in the index. Others feel substantive notes merit indexing. Others contend that in a "publish or perish" world, all notes should be indexed - even those that are merely bibliographic. I most frequently indicate notes this way: 142n18. Sometimes I don't italicize the n. There are an amazing number of variations on this.
There are also many variations on how to approach non-textual material such as illustrations, boxes, figures, and tables. If your indexing style guide doesn't state a preference, I generally italicize some or all of the page reference. If there are no boxes, figures or tables, and just illustrations, I may italicize the page reference. With more choices in non-textual material, I may italicize a letter to follow the page reference. Whatever method we decide upon, I will write a headnote to be placed at the beginning of the index that tells what these extra markings in the index mean.
Locators are usually, but not always, page numbers. In The Chicago Manual of Style the locators are a chapter number followed by a period followed by the paragraph number such as "18.109." URL addresses are another example of locators in websites, but most locators for books are page numbers.
Page numbers can be present in full, like this: 14-18, 243-247. Or they can be elided following Chicago or another style, like this for example: 100-104, 163-66, 193-209, 203-6, 209-212.
Volume numbers can be part of the locator as, for instance, II:14. Usually an en dash separates page ranges, but I can use a hyphen if you prefer - or any other character you specify.
Why use them and where to put them? First, there's no point in having a cross reference to a subject if there are fewer than five mentions of it in various places. In that instance, "double-posting" makes better sense. Why send the reader somewhere else, when the necessary locators don't take up a lot of space?
Cross references have many formatting options. Most often see and see also are italicized, but not always. Most often the initial letter is capitalized, but not always. They can be placed immediately following the main entry before or after any page numbers associated with it, or as the last subentry. The placement after the last subentry makes sense to me in run-in indexes, but not in intended indexes. In the latter I prefer placing the cross ref. after the main entry.
If there are any length limits for the index, it's imperative I know that at the outset. There are many ways to tighten up an index, some of which include using the run-in versus the indented format.
Indented indexes are easier to read than run-in indexes. An example:
dogs
foxhound, 134-135
Great Dane, 51-54
Setter, 239-241
Run-in index example:
Brooks, Henry, Jr., 167; arrives in Virginia, 181, 182-183; death of, 215; (J.) Glover and, 171; Ingle and, 214; Looking Glass and, 183, 186; surrenders to Ingle's men, 189; tobacco trade and, 169-170
Although run-in indexes are somewhat shorter than indented indexes, they often don't save a tremendous amount of space.
A sub-subentry is a third level in an index. They are not usually used in scholarly books with run-in indexes. Sub-subentries can be very helpful in some indented indexes but can be tricky to typeset. I am happy to proofread any typeset index I have written to make sure the indentations come out right. When they don't, the index doesn't make sense.
There are two major methods for sorting the entries of an index, "word-by-word" which is often used in library catalogs and encyclopedias, and "letter-by-letter" which is often used in dictionaries. Either is a setting in Cindex. I just need to know which style you prefer.