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roux-ohdsi · Apr 5, 2024 · f7e538c · f7e538c
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,6 +5,7 @@
 ^docs$
 ^pkgdown$
 ^README\.Rmd$
+^README\.qmd$
 ^data-raw$
 ^cran-comments\.md$
 ^\.github$

diff --git a/README.Rmd b/README.Rmd
@@ -16,19 +16,22 @@ knitr::opts_chunk$set(
 
 # `allofus` R Package
 
-The goal of the `allofus` R package is to streamline the use of R within the [All of Us Researcher Workbench](https://www.researchallofus.org/data-tools/workbench/).
-
-*The `allofus` R package is a not affiliated with or endorsed by the All of Us Research Program.*
-
-The `allofus` package helps researchers query the database and build transparent and reproducible analysed pipeline. The package allows researchers to easily use other database packages, such as `dbplyr` and `DBI`, with the All of Us database. The package also includes functions to help researchers manage storage in their workspace and bucket, as well as take advantage of tools developed for [OMOP CDM](https://www.researchallofus.org/faq/what-is-omop/) data.
-
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/roux-ohdsi/allofus/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/roux-ohdsi/allofus/actions/workflows/R-CMD-check.yaml)
 [![CRAN status](https://www.r-pkg.org/badges/version/allofus)](https://CRAN.R-project.org/package=allofus)
 [![](http://cranlogs.r-pkg.org/badges/grand-total/allofus)](https://cran.r-project.org/package=allofus)
 [![DOI](https://zenodo.org/badge/659848534.svg)](https://zenodo.org/doi/10.5281/zenodo.10420610)
 <!-- badges: end -->
 
+The goal of the `allofus` R package is to streamline the use of R within the [All of Us Researcher Workbench](https://www.researchallofus.org/data-tools/workbench/). It has 4 primary goals:
+
+1. Facilitate the use of popular `tidyverse` ecosystem of R packages on the Researcher Workbench
+2. Help researchers more efficiently and accurately extract and synthesize survey data and EHR data
+3. Increase the interoperability between tools created by the Observational Health Data Sciences and Informatics community (OHDSI) for the [OMOP CDM](https://www.researchallofus.org/faq/what-is-omop/)) and the Researcher Workbench
+4. Make connecting to the database and managing files simple 
+
+*The `allofus` R package was developed by Louisa Smith and Rob Cavanaugh at [Northeastern University](https://ohdsi.northeastern.edu) and is not affiliated with or endorsed by the All of Us Research Program.*
+
 ### Installation
 
 Install the released version of `allofus` from CRAN:
@@ -76,4 +79,4 @@ citation("allofus")
 
 ### Bugs
 
-Please leave us comments, requests, and report bugs using the "Issues" tab on github located here: https://github.com/roux-ohdsi/allofus/issues.
+Please leave us comments, requests, and report bugs using the "Issues" tab on github.
diff --git a/README.html b/README.html
diff --git a/README.md b/README.md
@@ -1,5 +1,4 @@
 
-
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # `allofus` R Package
@@ -8,8 +7,8 @@
 
 [![R-CMD-check](https://github.com/roux-ohdsi/allofus/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/roux-ohdsi/allofus/actions/workflows/R-CMD-check.yaml)
 [![CRAN
-status](https://www.r-pkg.org/badges/version/allofus.png)](https://CRAN.R-project.org/package=allofus)
-[![](http://cranlogs.r-pkg.org/badges/grand-total/allofus.png)](https://cran.r-project.org/package=allofus)
+status](https://www.r-pkg.org/badges/version/allofus)](https://CRAN.R-project.org/package=allofus)
+[![](http://cranlogs.r-pkg.org/badges/grand-total/allofus)](https://cran.r-project.org/package=allofus)
 [![DOI](https://zenodo.org/badge/659848534.svg)](https://zenodo.org/doi/10.5281/zenodo.10420610)
 <!-- badges: end -->
 
@@ -73,7 +72,6 @@ vignette to learn how to use the package.
 ### Citation
 
 Please cite the `allofus` package as:
-
 <p>
 Smith L, Cavanaugh R (2023). <em>allofus: Interface for ‘All of Us’
 Researcher Workbench</em>.

diff --git a/README.qmd b/README.qmd
@@ -1,4 +1,6 @@
-
+---
+default-image-extension: ""
+---
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 ```{r, include = FALSE}
@@ -14,18 +16,17 @@ knitr::opts_chunk$set(
 # `allofus` R Package
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/roux-ohdsi/allofus/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/roux-ohdsi/allofus/actions/workflows/R-CMD-check.yaml)
-[![CRAN status](https://www.r-pkg.org/badges/version/allofus)](https://CRAN.R-project.org/package=allofus)
-[![](http://cranlogs.r-pkg.org/badges/grand-total/allofus)](https://cran.r-project.org/package=allofus)
-[![DOI](https://zenodo.org/badge/659848534.svg)](https://zenodo.org/doi/10.5281/zenodo.10420610)
+
+[![R-CMD-check](https://github.com/roux-ohdsi/allofus/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/roux-ohdsi/allofus/actions/workflows/R-CMD-check.yaml) [![CRAN status](https://www.r-pkg.org/badges/version/allofus)](https://CRAN.R-project.org/package=allofus) [![](http://cranlogs.r-pkg.org/badges/grand-total/allofus)](https://cran.r-project.org/package=allofus) [![DOI](https://zenodo.org/badge/659848534.svg)](https://zenodo.org/doi/10.5281/zenodo.10420610)
+
 <!-- badges: end -->
 
 The goal of the `allofus` R package is to streamline the use of R within the [All of Us Researcher Workbench](https://www.researchallofus.org/data-tools/workbench/). It has 4 primary goals:
 
-1. Facilitate the use of popular `tidyverse` ecosystem of R packages on the Researcher Workbench
-2. Help researchers more efficiently and accurately extract and synthesize survey data and EHR data
-3. Increase the interoperability between tools created by the Observational Health Data Sciences and Informatics community (OHDSI) for the [OMOP CDM](https://www.researchallofus.org/faq/what-is-omop/)) and the Researcher Workbench
-4. Make connecting to the database and managing files simple 
+1.  Facilitate the use of popular `tidyverse` ecosystem of R packages on the Researcher Workbench
+2.  Help researchers more efficiently and accurately extract and synthesize survey data and EHR data
+3.  Increase the interoperability between tools created by the Observational Health Data Sciences and Informatics community (OHDSI) for the [OMOP CDM](https://www.researchallofus.org/faq/what-is-omop/)) and the Researcher Workbench
+4.  Make connecting to the database and managing files simple
 
 *The `allofus` R package was developed by Louisa Smith and Rob Cavanaugh at [Northeastern University](https://ohdsi.northeastern.edu) and is not affiliated with or endorsed by the All of Us Research Program.*
 
@@ -44,8 +45,7 @@ install.packages("pak")
 pak::pak("roux-ohdsi/allofus")
 ```
 
-On the new RStudio interface on the workbench, you will need to manually specify
-the CRAN mirror to be able to download *any* recently updated packages. 
+On the new RStudio interface on the workbench, you will need to manually specify the CRAN mirror to be able to download *any* recently updated packages.
 
 ```{r}
 # specify the mirror directly
@@ -66,10 +66,13 @@ Read through the [getting started](https://roux-ohdsi.github.io/allofus/articles
 ### Citation
 
 Please cite the `allofus` package as:
+
 ```{r, results = "asis", echo = FALSE, eval = TRUE}
 print(citation("allofus"), style = "html")
 ```
+
 or with
+
 ```{r}
 citation("allofus")
 ```