From ecd84cb5181e90a21c082ed2d53e76bcc4d40cdd Mon Sep 17 00:00:00 2001 From: Matthew Hamilton Date: Mon, 12 Sep 2022 13:11:00 +1000 Subject: [PATCH] rebuilt all vignettes --- vignettes/CSP_AQOL6D_TTU.Rmd | 4 +-- vignettes/CSP_EQ5D_TTU.Rmd | 4 +-- vignettes/Model_TTU.Rmd | 22 +++++++-------- vignettes/TTU.Rmd | 52 ++++++++++++++++++------------------ vignettes/V_01.Rmd | 7 ++++- vignettes/aaaaaaaaaa.txt | 0 6 files changed, 47 insertions(+), 42 deletions(-) delete mode 100644 vignettes/aaaaaaaaaa.txt diff --git a/vignettes/CSP_AQOL6D_TTU.Rmd b/vignettes/CSP_AQOL6D_TTU.Rmd index 4a156bbb..b12126d0 100644 --- a/vignettes/CSP_AQOL6D_TTU.Rmd +++ b/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} --- diff --git a/vignettes/CSP_EQ5D_TTU.Rmd b/vignettes/CSP_EQ5D_TTU.Rmd index bd392a66..33fc03f4 100644 --- a/vignettes/CSP_EQ5D_TTU.Rmd +++ b/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} --- diff --git a/vignettes/Model_TTU.Rmd b/vignettes/Model_TTU.Rmd index f51fb720..43060db0 100644 --- a/vignettes/Model_TTU.Rmd +++ b/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---- - -**The workflow previously described on this page is now defunct as the functions it relied on have been superseded by methods in the [specific package](https://ready4-dev.github.io/specific).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).** + diff --git a/vignettes/TTU.Rmd b/vignettes/TTU.Rmd index 84109a71..0e21f319 100644 --- a/vignettes/TTU.Rmd +++ b/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) + + + diff --git a/vignettes/V_01.Rmd b/vignettes/V_01.Rmd index 0f4c68c0..a038db16 100644 --- a/vignettes/V_01.Rmd +++ b/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", diff --git a/vignettes/aaaaaaaaaa.txt b/vignettes/aaaaaaaaaa.txt deleted file mode 100644 index e69de29b..00000000