Add option to use ATLAS Pathways SQL

[katy-sadowski]

• Adds the original Pathways SQL query from ATLAS, and a parameter in createTxHistoryTable that lets the user choose this or the default query. Defaults to default to avoid a breaking change
  • Users will need to re-run their code from the start once the update the package, but won't need to update any code
• Adds warnings in spots where the ATLAS output is not suitable (i.e., when end dates are used in the analysis). The ATLAS approach collapses all dates, including end dates in certain cases, so its end dates are not usable in analysis
• Adds documentation about the 2 approaches
• Resolves R CMD Check WARNINGs. There are still lots of NOTEs to clean up