Merge branch 'main' into add-user-error-message-for-missing-strata

README.md

@@ -9,6 +9,7 @@
 
 [![R-CMD-check](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/UCD-SERG/serocalculator/graph/badge.svg?token=85CXV6GN2T)](https://codecov.io/gh/UCD-SERG/serocalculator)
+
 <!-- badges: end -->
 
 Antibody levels measured in a cross–sectional population sample can be
@@ -29,11 +30,13 @@ Started](https://ucd-serg.github.io/serocalculator/articles/serocalculator.html)
 
 ## Installing R
 
-The **serocalculator** package is written in R, a free, open-source
-software program. The end user of this package must have access to a
-working installation of the R software. We recommend installing [base
-R](https://cran.r-project.org/) and a Graphical User Interfaces (GUI)
-for R such as [RStudio](https://posit.co/products/open-source/rstudio/).
+The **serocalculator** package is designed for use in
+[R](https://www.r-project.org/), which is a free, open-source software
+environment for statistical computing and graphics. The end user of this
+package must have access to a working installation of the R software. We
+recommend installing [base R](https://cran.r-project.org/) and a
+Graphical User Interface (GUI) for R such as
+[RStudio](https://posit.co/products/open-source/rstudio/).
 
 If you need to download and install R and/or RStudio, we recommend
 following the tutorial below from *Hands On Programming in R* by Garrett
@@ -94,8 +97,11 @@ devtools::install_github("ucd-serg/serocalculator")
 Before launching the development version of **serocalculator**, Windows
 users will need to install Rtools, which contains a collection of tools
 for building and employing R packages that are still in development.
-This can be done either: (1) during the *devtools* package installation,
-**or** (2) independently if *devtools* is already installed.
+This can be done either: 
+
+(1) [during the *devtools* package
+installation](#during-devtools-installation), **or** 
+(2) [independently](#independently), if *devtools* is already installed.
 
 ##### During devtools installation
 
@@ -126,10 +132,21 @@ package](man/figures/Rtools1.png)
 
 ## Getting Help
 
-If you need assistance or encounter a clear bug, please file an issue
-with a minimal reproducible example on
+If you have questions about using this software package, please use the
+[Q&A
+forum](https://github.com/UCD-SERG/serocalculator/discussions/categories/q-a).
+
+If you encounter a clear bug, please file an issue with a [minimal
+reproducible example](https://reprex.tidyverse.org/) on
 [GitHub](https://github.com/UCD-SERG/serocalculator/issues).
 
 Another great resource is **The Epidemiologist R Handbook**, which
 includes an introductory page on asking for help with R packages via
 GitHub: https://epirhandbook.com/en/getting-help.html
+
+## Contributing to this project
+
+We welcome contributions to this project - anything from typo
+corrections to new features. Please see our [Contributor
+guide](https://ucd-serg.github.io/serocalculator/CONTRIBUTING.html#fixing-typos)
+for more information.

README.qmd

@@ -23,14 +23,21 @@ knitr::opts_chunk$set(
 <!-- badges: end -->
 
 
-Antibody levels measured in a cross–sectional population sample can be translated into an estimate of the frequency with which seroconversions (infections) occur in the sampled population. In other words, the presence of many high antibody titers indicates that many individuals likely experienced infection recently and the burden of disease is high in the population, while low titers indicate a low frequency of infections in the sampled population and therefore a lower burden of disease.
+Antibody levels measured in a cross–sectional population sample can be translated into an estimate of the frequency with which seroconversions (infections) occur in the sampled population. 
+In other words, the presence of many high antibody titers indicates that many individuals likely experienced infection recently and the burden of disease is high in the population, 
+while low titers indicate a low frequency of infections in the sampled population and therefore a lower burden of disease.
 
-The **serocalculator** package was designed to use the longitudinal response characteristics using a set of modeled parameters characterizing the longitudinal response of the selected serum antibodies. More details on the underlying methods can be found in [Getting Started](https://ucd-serg.github.io/serocalculator/articles/serocalculator.html).
+The **serocalculator** package was designed to use the longitudinal response characteristics 
+using a set of modeled parameters characterizing the longitudinal response of the selected serum antibodies. 
+More details on the underlying methods can be found in [Getting Started](https://ucd-serg.github.io/serocalculator/articles/serocalculator.html).
 
 
 ## Installing R
 
-The **serocalculator** package is written in R, a free, open-source software program. The end user of this package must have access to a working installation of the R software. We recommend installing [base R](https://cran.r-project.org/) and a Graphical User Interfaces (GUI) for R such as [RStudio](https://posit.co/products/open-source/rstudio/).
+The **serocalculator** package is designed to be used in [R](https://www.r-project.org/), 
+which is a free, open-source software environment for statistical computing and graphics. 
+The end user of this package must have access to a working installation of the R software. 
+We recommend installing [base R](https://cran.r-project.org/) and a Graphical User Interface (GUI) for R such as [RStudio](https://posit.co/products/open-source/rstudio/).
 
 If you need to download and install R and/or RStudio, we recommend following the tutorial below from *Hands On Programming in R* by Garrett Grolemund:
 
@@ -78,10 +85,10 @@ devtools::install_github("ucd-serg/serocalculator")
 ```
 #### A Note for Windows Users
 
-Before launching the development version of **serocalculator**, Windows users will need to install Rtools, which contains a collection of tools for building and employing R packages that are still in development. This can be done either: (1) during the *devtools* package installation, **or** (2) independently if *devtools* is already installed.
+Before launching the development version of **serocalculator**, Windows users will need to install Rtools, which contains a collection of tools for building and employing R packages that are still in development. 
+This can be done either: (1) [during the *devtools* package installation](#during-devtools-installation), **or** (2) [independently](#independently), if *devtools* is already installed.
 
-
-##### During devtools installation {#sec-install-rtools-with-devtools}
+##### During devtools installation
 
 When prompted to install additional build tools, select "Yes" and Rtools will be installed. 
 
@@ -93,7 +100,7 @@ When prompted to install additional build tools, select "Yes" and Rtools will be
 After installing Rtools, you may need to restart RStudio before continuing to install `serocalculator`.
 :::
 
-##### Independently: {#sec-install-rtools-a-la-carte}
+##### Independently:
 
 1. Download Rtools from https://cran.r-project.org/bin/windows/Rtools/
 2. Run the installer
@@ -106,7 +113,21 @@ After installing Rtools, you may need to restart RStudio before continuing to in
 
 ## Getting Help
 
-If you need assistance or encounter a clear bug, please file an issue with a minimal reproducible example on [GitHub](https://github.com/UCD-SERG/serocalculator/issues). 
+If you have questions about using this software package,
+please use the [Q&A forum](https://github.com/UCD-SERG/serocalculator/discussions/categories/q-a).
+
+If you encounter a clear bug, please file an issue 
+with a [minimal reproducible example](https://reprex.tidyverse.org/)
+on [GitHub](https://github.com/UCD-SERG/serocalculator/issues). 
+
+Another great resource is **The Epidemiologist R Handbook**, 
+which includes an introductory page on asking for help with R packages via GitHub: 
+https://epirhandbook.com/en/getting-help.html
 
-Another great resource is **The Epidemiologist R Handbook**, which includes an introductory page on asking for help with R packages via GitHub: https://epirhandbook.com/en/getting-help.html
+## Contributing to this project
 
+We welcome contributions to this project - 
+anything from typo corrections to new features. 
+Please see our 
+[Contributor guide](https://ucd-serg.github.io/serocalculator/CONTRIBUTING.html#fixing-typos) 
+for more information.