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

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

vignettes/derived_variables.qmd

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

vignettes/get_started.qmd

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

vignettes/how_to_add_variables.qmd

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

vignettes/recoding_medications.qmd

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

vignettes/tagged_na_usage.qmd

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

vignettes/variable_details.qmd

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

vignettes/variables_sheet.qmd

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

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