Fixed Suggests of DESCRIPTION and vingette fields of qmds to resolve CMD, lint, and hopefully pkgdown checks

Author: rafdoodle

DESCRIPTION

@@ -23,6 +23,6 @@ BugReports: https://github.com/Big-Life-Lab/chmsflow/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Suggests: dplyr, DT, kableExtra, readr, recodeflow, testthat (>= 3.0.0)
+Suggests: dplyr, DT, kableExtra, knitr, quarto, readr, recodeflow, testthat (>= 3.0.0)
 VignetteBuilder: quarto
 LazyData: true

vignettes/derived_variables.qmd

@@ -1,6 +1,10 @@
 ---
 title: "Derived variables"
 format: html
+vignette: >
+  %\VignetteIndexEntry{Derived variables}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r setup, include=FALSE}

vignettes/get_started.qmd

@@ -1,6 +1,10 @@
 ---
 title: "Get started"
 format: html
+vignette: >
+  %\VignetteIndexEntry{Get started}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ## 1. Load packages

vignettes/how_to_add_variables.qmd

@@ -1,6 +1,10 @@
 ---
 title: "How to add variables to chmsflow"
 format: html
+vignette: >
+  %\VignetteIndexEntry{How to add variables to chmsflow}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r setup, include=FALSE}

vignettes/recoding_medications.qmd

@@ -1,6 +1,10 @@
 ---
 title: "Recoding CHMS medication variables"
 format: html
+vignette: >
+  %\VignetteIndexEntry{Recoding CHMS medication variables}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ## 1. Load packages

vignettes/tagged_na_usage.qmd

@@ -1,6 +1,10 @@
 ---
 title: "missing data (tagged_na)"
 format: html
+vignette: >
+  %\VignetteIndexEntry{missing data (tagged_na)}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r setup, include=FALSE}

vignettes/variable_details.qmd

@@ -1,6 +1,10 @@
 ---
 title: "variable_details.csv"
 format: html
+vignette: >
+  %\VignetteIndexEntry{variable_details.csv}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r setup, include=FALSE}
@@ -166,5 +170,3 @@ The same naming convention applies to derived variables with the exception of tw
 
 2. In **recEnd**, write **Func::** followed with the name of the custom function used to create the derived variable.
 + `Func::derivedFunction`
-
-```

vignettes/variables_sheet.qmd

@@ -1,6 +1,10 @@
 ---
 title: "variables.csv"
 format: html
+vignette: >
+  %\VignetteIndexEntry{variables.csv}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r setup, include=FALSE}
@@ -19,15 +23,15 @@ Read `variables.csv`
 ```{r Read variables.csv, echo=FALSE, message=FALSE, warning=FALSE}
 library(chmsflow)
 
-catalogue(
+cat(
   "There are", nrow(variables), "variables, grouped in", sum(!duplicated(variables$subject)),
   "subjects and", sum(!duplicated(variables$section)), "sections that are available for
     transformation in CHMS cycles 1-6.", "\n\n"
 )
 ```
 
 ```{r, echo=FALSE}
-catalogue(
+cat(
   "You can search for variables in the table below. Try searching for the",
   sum(variables$subject == "Age"), "age variables that are used in the Transform
     CHMS variables vignette. All", sum(variables$subject == "Age"),