rebuilt all vignettes

Author: matthewphamilton

vignettes/CSP_AQOL6D_TTU.Rmd

@@ -1,8 +1,8 @@
 ---
-title: "AQoL-6D Clinical Population Example (Deprecated)"
+title: "(Defunct) AQoL-6D Clinical Population Example"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{AQoL-6D Clinical Population Example (Deprecated)}
+  %\VignetteIndexEntry{(Defunct) AQoL-6D Clinical Population Example}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

vignettes/CSP_EQ5D_TTU.Rmd

@@ -1,8 +1,8 @@
 ---
-title: "EQ5D General Population Example (Deprecated)"
+title: "(Defunct) EQ5D General Population Example"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{EQ5D General Population Example (Deprecated)}
+  %\VignetteIndexEntry{(Defunct) EQ5D General Population Example}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

vignettes/Model_TTU.Rmd

@@ -1,11 +1,11 @@
----
-title: "Exploratory Analysis Workflow"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{Exploratory Analysis Workflow}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-**The workflow previously described on this page is now defunct as the functions it relied on have been superseded by methods in the [specific package](https://ready4-dev.github.io/specific). Updated syntax for reporting utility mapping studies with the TTU package is currently being developed.**
-
+---
+title: "(Defunct) Exploratory Analysis Workflow"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{(Defunct) Exploratory Analysis Workflow}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+**The workflow previously described on this page is now defunct as the functions it relied on have been superseded by methods in the [specific package](https://ready4-dev.github.io/specific).**
+

vignettes/TTU.Rmd

@@ -1,26 +1,26 @@
----
-title: "TTU"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{TTU}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-```{r, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-```
-
-```{r setup}
-library(TTU)
-```
-
-**The TTU package is currently undergoing significant redevelopment. Many of the functions previously included in the package have been replaced by methods in the [specific package](https://ready4-dev.github.io/specific).  More information will be poster here shortly.** 
-
-This development version of the TTU package has been made available as part of the process of testing and documenting the package. [Installation instructions are on the package homepage](https://ready4-dev.github.io/TTU/index.html).
-
-
-
+---
+title: "TTU"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{TTU}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup, message=FALSE, warning=FALSE, results='hide'}
+library(TTU)
+```
+
+This development version of the TTU package has been made available as part of the process of testing and documenting the package. [Installation instructions are on the package homepage](https://ready4-dev.github.io/TTU/index.html). Currently, one vignette article is available to demonstrate how to use the TTU package:
+
+- [Implement A Utility Mapping Study (Adolescent AQoL-6D Example)](V_01.html)
+
+
+

vignettes/V_01.Rmd

@@ -33,6 +33,7 @@ Additionally, TTU relies on two RMarkdown programs:
 ### Background and citation 
 The following workflow illustrates (**using fake data**) the same steps we used in a real world study, a summary of which is available at https://doi.org/10.1101/2021.07.07.21260129). Citation information for that study is:
 
+```{r eval=F}
 @article {Hamilton2021.07.07.21260129,
 	author = {Hamilton, Matthew P and Gao, Caroline X and Filia, Kate M and Menssink, Jana M and Sharmin, Sonia and Telford, Nic and Herrman, Helen and Hickie, Ian B and Mihalopoulos, Cathrine and Rickwood, Debra J and McGorry, Patrick D and Cotton, Sue M},
 	title = {Predicting Quality Adjusted Life Years in young people attending primary mental health services},
@@ -44,9 +45,11 @@ The following workflow illustrates (**using fake data**) the same steps we used
 	eprint = {https://www.medrxiv.org/content/early/2021/07/12/2021.07.07.21260129.full.pdf},
 	journal = {medRxiv}
 }
+```
 
 The program applied in that study, which this workflow closely resembles is available at https://doi.org/10.5281/zenodo.6116077 and can be cited as follows:
 
+```{r eval=FALSE}
 @software{hamilton_matthew_2022_6212704,
   author       = {Hamilton, Matthew and
                   Gao, Caroline},
@@ -68,6 +71,8 @@ The program applied in that study, which this workflow closely resembles is avai
   doi          = {10.5281/zenodo.6212704},
   url          = {https://doi.org/10.5281/zenodo.6212704}
 }
+```
+
 
 ### Load required packages
 We begin by loading our required packages.
@@ -175,7 +180,7 @@ A <- renewSlot(A, "c_SpecificProject",
                authorSlot(A, "c_SpecificProject", what_1L_chr = "workspace"))
 ```
 
-We now generate tables and charts that describe our dataset. These are saved in a sub-directory of our output data directory, a copy of which is [available for download](https://github.com/ready4-dev/TTU/releases/download/Documentation_0.0/_A_Candidate_Mdls_Cmprsn_Descriptives.zip). One of the plots is also reproduced here.
+We now generate tables and charts that describe our dataset. These are saved in a sub-directory of our output data directory, a copy of which is [available for download](https://github.com/ready4-dev/TTU/releases/download/Documentation_0.0/_Descriptives.zip). One of the plots is also reproduced here.
 
 ```{r message=FALSE, results='hide', warning=FALSE}
 A <- renewSlot(A, "c_SpecificProject",