I agree completely with @Kurt_Bremser and his step 1 is so important, I'm going to repeat it with a slight modification in italics
create non-macro code that works for at least two departments
Why? Because if you can't get the reports to work without macros, you will never get the reports to work with macros. Many people ignore this advice. Don't be one of those people.
Macros that are dynamic: I'm having trouble adding conditional logic for various output formats to the macro I've started writing that loops through the department names.
Does not %IF-%THEN %DO-%END provide the logic needed here?
Visual Exporting: Even though I know how to use PROC SGPLOT to create graphs, I'm not sure how to combine them with tables in a single PDF.
ODS PDF does this for you.
Folder management: Using department names to automate the creation and saving of reports into designated directories.
Macro variable with appropriate folder names ought to do this. Use that macro variable in the ODS PDF command.
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How should macros be organized for a report this dynamic?
Organized? Each macro could be in its own .SAS file with appropriate file name to identify the macro.
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Are there any particular steps or settings in SAS that make exporting tables and graphics together easier?
The ODS PDF command has everything you need. It's pretty simple really. use the ODS PDF command before the first table or graph, and then ODS PDF CLOSE after the last table or graph.
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Does anyone have any examples of successful conditional formatting in macros?
Conditional formatting hasn't been mentioned before in your problem statement, but this is easily done via PROC REPORT or PROC TABULATE. It doesn't have to be a function of macros.
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Paige Miller