Update readme and vignettes

Author: shannarucker

README.Rmd

@@ -34,12 +34,14 @@ devtools::install_github("LimnoTech/SCI")
 
 Produce the SCI scores in just a few simple steps:
 
-1.  In RStudio, open the [workflow.R](https://github.com/LimnoTech/SCI/blob/master/workflow.R) script.
+1.  Complete the [pre-processing steps](https://limnotech.github.io/SCI/articles/pre-processing.html), as needed.
 
-2.  Update the "Input Variables" section of the script and confirm the latest data files are saved in the [data](https://github.com/LimnoTech/SCI/tree/master/data) folder.
+2.  In RStudio, open the [workflow.R](https://github.com/LimnoTech/SCI/blob/master/workflow.R) script.
 
-3.  Update [lookup_tables.xlsx](https://github.com/LimnoTech/SCI/blob/master/data/lookup_tables.xlsx) and run code from the "Lookup Tables" section of the script, as needed. Note: this step is not typically necessary.
+3.  Update the "Input Variables" section of the script and confirm the latest data files are saved in the [data](https://github.com/LimnoTech/SCI/tree/master/data) folder.
 
-4.  Click the Source button to run the script.
+4.  Update [lookup_tables.xlsx](https://github.com/LimnoTech/SCI/blob/master/data/lookup_tables.xlsx) and run code from the "Lookup Tables" section of the script, as needed. Note: this step is not typically necessary.
 
-5.  View the results in [all_scores.csv](https://github.com/LimnoTech/SCI/blob/master/all_scores.csv).
+5.  Click the Source button to run the workflow.R script.
+
+6.  View the results in [all_scores.csv](https://github.com/LimnoTech/SCI/blob/master/all_scores.csv).

README.md

@@ -24,20 +24,24 @@ devtools::install_github("LimnoTech/SCI")
 
 Produce the SCI scores in just a few simple steps:
 
-1.  In RStudio, open the
+1.  Complete the [pre-processing
+    steps](https://limnotech.github.io/SCI/articles/pre-processing.html),
+    as needed.
+
+2.  In RStudio, open the
     [workflow.R](https://github.com/LimnoTech/SCI/blob/master/workflow.R)
     script.
 
-2.  Update the “Input Variables” section of the script and confirm the
+3.  Update the “Input Variables” section of the script and confirm the
     latest data files are saved in the
     [data](https://github.com/LimnoTech/SCI/tree/master/data) folder.
 
-3.  Update
+4.  Update
     [lookup_tables.xlsx](https://github.com/LimnoTech/SCI/blob/master/data/lookup_tables.xlsx)
     and run code from the “Lookup Tables” section of the script, as
     needed. Note: this step is not typically necessary.
 
-4.  Click the Source button to run the script.
+5.  Click the Source button to run the workflow.R script.
 
-5.  View the results in
+6.  View the results in
     [all_scores.csv](https://github.com/LimnoTech/SCI/blob/master/all_scores.csv).