Revise R markdown related to reusing chunks

[brandon-gallas]

Si provided the following feedback,

When I run the 20210505_PathInformatics-Gallas.Rmd, there is an error on Line 457-- Error: unexpected input in <<. It seems that the code is incomplete. It also happens on Line 478 and the last 5 chunks.

The << input only works when you knit the R markdown file. It doesn't work when you run the code like a script. Let's find a better way to reuse code so that it works when the code is run like a script.

Brandon