UCD-SERG · d-morrison · Jul 10, 2024 · Jul 3, 2024 · Jul 4, 2024 · Jul 5, 2024
diff --git a/README.md b/README.md
@@ -1,136 +1,135 @@
-# serocalculator
-
-
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
-------------------------------------------------------------------------
-
-<!-- badges: start -->
-
-[![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)
-<!-- 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.
-
-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/).
-
-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:
-
-**Installing R and RStudio**:
-https://rstudio-education.github.io/hopr/starting.html
-
-## Installing the Serocalculator Package
-
-The **serocalculator** package must be installed in R before first use.
-
-``` r
-# Install package
-install.packages("serocalculator")
-```
-
-### Post-installation
-
-Successful installation can be confirmed by loading the package into the
-RStudio workspace and exploring help files and manuals distributed with
-the package:
-
-``` r
-# Load package "seroincidence".
-library(serocalculator)
-
-# Show R help for the package.
-?serocalculator
-```
-
-Additionally, most package details can be found when executing the
-following commands:
-
-``` r
-# Show description.
-packageDescription("serocalculator")
-
-# Show citation.
-citation("serocalculator")
-```
-
-### Development Version
-
-To install the development version, you must install the **devtools** R
-package and then download **serocalculator** from
-[GitHub](https://github.com/). Enter the code below into the R console
-to install both packages.
-
-``` r
-# Install the devtools package and the development version of serocalculator
-install.packages("devtools")
-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](#sec-install-rtools-with-devtools), **or** (2)
-[independently if *devtools* is already
-installed](#sec-install-rtools-a-la-carte).
-
-##### During devtools installation
-
-When prompted to install additional build tools, select “Yes” and Rtools
-will be installed.
-
-![Click Yes to install Rtools along with the *devtools*
-package](man/figures/Rtools1.png)
-
-> [!NOTE]
->
-> After installing Rtools, you may need to restart RStudio before
-> continuing to install `serocalculator`.
-
-##### Independently:
-
-1.  Download Rtools from https://cran.r-project.org/bin/windows/Rtools/
-
-2.  Run the installer
-
-    - During the Rtools installation you may see a window asking you to
-      “Select Additional Tasks”.
-    - Do **not** select the box for “Edit the system PATH”. devtools and
-      RStudio should put Rtools on the PATH automatically when it is
-      needed.
-    - **Do** select the box for “Save version information to registry”.
-      It should be selected by default.
-
-## 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).
-
-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
+# serocalculator
+
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+------------------------------------------------------------------------
+
+<!-- badges: start -->
+
+[![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
+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).
+
+## 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/).
+
+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:
+
+**Installing R and RStudio**:
+https://rstudio-education.github.io/hopr/starting.html
+
+## Installing the Serocalculator Package
+
+The **serocalculator** package must be installed in R before first use.
+
+``` r
+# Install package
+install.packages("serocalculator")
+```
+
+### Post-installation
+
+Successful installation can be confirmed by loading the package into the
+RStudio workspace and exploring help files and manuals distributed with
+the package:
+
+``` r
+# Load package "seroincidence".
+library(serocalculator)
+
+# Show R help for the package.
+?serocalculator
+```
+
+Additionally, most package details can be found when executing the
+following commands:
+
+``` r
+# Show description.
+packageDescription("serocalculator")
+
+# Show citation.
+citation("serocalculator")
+```
+
+### Development Version
+
+To install the development version, you must install the **devtools** R
+package and then download **serocalculator** from
+[GitHub](https://github.com/). Enter the code below into the R console
+to install both packages.
+
+``` r
+# Install the devtools package and the development version of serocalculator
+install.packages("devtools")
+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.
+
+##### During devtools installation
+
+When prompted to install additional build tools, select “Yes” and Rtools
+will be installed.
+
+![Click Yes to install Rtools along with the *devtools*
+package](man/figures/Rtools1.png)
+
+> [!NOTE]
+>
+> After installing Rtools, you may need to restart RStudio before
+> continuing to install `serocalculator`.
+
+##### Independently:
+
+1.  Download Rtools from https://cran.r-project.org/bin/windows/Rtools/
+
+2.  Run the installer
+
+    - During the Rtools installation you may see a window asking you to
+      “Select Additional Tasks”.
+    - Do **not** select the box for “Edit the system PATH”. devtools and
+      RStudio should put Rtools on the PATH automatically when it is
+      needed.
+    - **Do** select the box for “Save version information to registry”.
+      It should be selected by default.
+
+## 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).
+
+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
diff --git a/README.qmd b/README.qmd
@@ -19,6 +19,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![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 -->