Merge pull request #189 from FredHutch/note-nab-template-existence-in…

…-documentation

Note nab template existence in documentation

README.Rmd

@@ -78,7 +78,7 @@ Use a VISC Report:
 use_visc_report(
   report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file
   path = "BAMA", # the path within the active directory, usually the name of the assay
-  report_type = "bama" # "empty", "generic", or "bama" 
+  report_type = "bama" # "empty", "generic", "bama", or "nab"
 )
 ```
 

README.md

@@ -5,10 +5,10 @@
 
 The goal of VISCtemplates is to:
 
--   automate project setup
--   provide a common, easy-to-understand directory structure across
-    analyses
--   provide consistency across VISC reports
+- automate project setup
+- provide a common, easy-to-understand directory structure across
+  analyses
+- provide consistency across VISC reports
 
 ## Installation
 
@@ -23,13 +23,12 @@ remotes::install_github("FredHutch/VISCtemplates", build_vignettes = TRUE)
 
 ## Requirements
 
--   R (version >= 3.0)
--   RStudio (version >= 1.2)
-    -   Includes Pandoc (version >= 2.0), which is needed for Word
-        reports.
--   TinyTeX (or MiKTeX), which is needed for PDF reports.
-    -   `install.packages(“tinytex”)`
-    -   `tinytex::install_tinytex()`
+- R (version \>= 3.0)
+- RStudio (version \>= 1.2)
+  - Includes Pandoc (version \>= 2.0), which is needed for Word reports.
+- TinyTeX (or MiKTeX), which is needed for PDF reports.
+  - `install.packages(“tinytex”)`
+  - `tinytex::install_tinytex()`
 
 ## Vignettes
 
@@ -69,7 +68,7 @@ Use a VISC Report:
 use_visc_report(
   report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file
   path = "BAMA", # the path within the active directory, usually the name of the assay
-  report_type = "bama" # "empty", "generic", or "bama" 
+  report_type = "bama" # "empty", "generic", "bama", or "nab"
 )
 ```
 

vignettes/using_pdf_and_word_template.Rmd

@@ -1,6 +1,5 @@
 ---
 title: "Using a VISC Report Template"
-author: Jimmy Fulp and Monica Gerber
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
@@ -16,19 +15,21 @@ There are a few different types of reports available:
 * **empty**: A blank report template that includes the VISC header, but no other text.
 * **generic**: A PT report template that includes generic text that can be adapted to your statistical analysis.
 * **bama**: A PT report template for the BAMA assay.
+* **nab**: A PT report template for the NAb assay.
 
 To use a VISC report template, run:
 
 ```{r eval=FALSE}
 use_visc_report(
   report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file
   path = "BAMA", # the path within the active directory, usually the name of the assay
-  report_type = "bama" # "empty", "generic", or "bama" 
+  report_type = "bama" # "empty", "generic", "bama", or "nab"
 )
 ```
 
-If you choose `report_type = "generic"` or `report_type = "bama"`, this will set 
-up the following structure in the existing `BAMA/` directory:
+If you choose any `report_type` other than `"empty"`, this will set 
+up a specific structure in the directory specified in `path`. Continuing with the BAMA
+example above, this structure looks like:
 
 ```
 |- BAMA/
@@ -87,7 +88,8 @@ There are some new functions and coding conventions that help with knitting the
 
 **References/Bibliography**
 
-*  For referencing papers, simply use the @ symbol before bib file reference (i.e. `@Huang:2013fl`).
+*  For referencing papers inline, simply use the @ symbol before bib file reference (e.g., "As specified in `@Huang:2013fl`, ...").
+*  For referencing papers in parentheses at the end of a sentence, use brackets and the @ symbol (e.g., `[@Huang:2013fl]`). The parentheses will be automatically included - do not add any extra.
 
 ### Tables