Update setup

[gcperk]

Hey @ateucher , I updated PEMprepr and PEMr to rework the format and continued to add more functions. I tracked my key notes/questions and things to consider here. I checked with @ccarmour's workflow script to incorporate any sticky pts, although these seem mainly to be with checking input/output and file structure, so i think we have most of these covered off now. Key updates:

• converted vignette back to .RMD and move to PEMr package with a skeleton pipeline/workflow (still to be filled out in detail).
• convert core templates back to .R and added scripts to show functions as placeholders in order
• added functions: create_vectors, create_raster_template, create_covariates and get_cded_dem.
• added placeholder tests for the above.
• I left a placeholder for @ccarmour's lidar processing script updates to be added when complete.

It would be great to get your input on these two pull requests before i get too far down the rabbit hole. Thanks!

@ccarmour and @whmacken - tagging you both to keep you in the loop, no need for input at this time.

[gcperk]

hi @ateucher, I like your idea to split this into two reviews. I have made the requested changes to get the rmd check to work. Although there is still an undefined variable "data" in the utils.R . I think this function would require a bit more thought as it also relates to the .rda files. Perhaps a neater way to compact this. I am passing this back to you with a few notes on outstanding tasks for me to complete. Thanks again for your input.