diff --git a/README.md b/README.md index 43c28768..42bfcf5e 100644 --- a/README.md +++ b/README.md @@ -1,136 +1,135 @@ -# serocalculator - - - - ------------------------------------------------------------------------- - - - -[![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) - - -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 + + + + +------------------------------------------------------------------------ + + + +[![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) + + +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 index daa98bbb..120445fb 100644 --- a/README.qmd +++ b/README.qmd @@ -19,6 +19,7 @@ knitr::opts_chunk$set( [![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)