SeroTrackR

The {SeroTrackR} R package compliments the PvSeroApp see Github here for experienced users who are comfortable with implementing the code in their own R sessions.

This package contains helper functions relevant for Plasmodium spp. projects for in-house and collaborator needs.

How to install the package:

{r} # Download the package available on the Comprehensive R Archive Network (CRAN) install.packages("SeroTrackR") # Load the package in your R session library(SeroTrackR)

Alternatively, you can download the developmental version on GitHub.

{r} pak::pak("dionnecargy/SeroTrackR") library(SeroTrackR) # To load the package

The GitHub (master) version also bundles the trained classification model file locally, whereas the CRAN version downloads it from this repository at runtime, so the CRAN version requires an internet connection the first time functions such as classifyResults() are called.

Dependencies

Package dependencies are installed automatically by install.packages() or pak::pak(). If you are missing system libraries needed to build a dependency from source (e.g. curl, openssl, xml2 on Linux), pak::pak() will usually install the required system requirements for you; otherwise install the appropriate system package for your OS first.

Documentation

Two sites serve different purposes:

• ebook: the comprehensive guide: end-to-end workflows for the fit-for-purpose tool described in Argyropoulos et al. 2026 VeriXiv and for pathogen-agnostic uses. Start here if you’re learning the package.
• pkgdown site: the reference: function documentation, arguments, and the vignettes as articles. Use this for quick lookups.

The same vignettes are also available offline inside R:

```{r} browseVignettes(“SeroTrackR”)

To run a specific vignette:

vignette(“PvSeroApp_R_Tutorial”) vignette(“Pk_Pv_Pf_Serology_Tutorial”) ```

Citing SeroTrackR

If you use SeroTrackR in your work, please cite both the pre-print describing the method and the package itself:

Argyropoulos D, Conway E, Bourke C, Li-Wai-Suen C, Ruybal-Pesántez S, Smith L, Mueller I, Longley R. PvSeroApp and SeroTrackR: An automated pipeline for Plasmodium vivax malaria serological analyses and machine learning classification of recent exposure. VeriXiv 2026; 3:313. https://doi.org/10.12688/verixiv.3797.2

SeroTrackR R package (CRAN): https://doi.org/10.32614/CRAN.package.SeroTrackR

Run citation("SeroTrackR") in R to get both entries in BibTeX format.

The source code of each release is additionally archived on Zenodo for long-term preservation; the preferred citations are the two above.

If you are using the {PvSeroApp} in your work, please cite:

Smith L, Argyropoulos DC, Bareng APN, Lin J, Kiernan-Walker N, Lamont M, Abraham A, Lim PS, Wu KW, William T, Anstey NM, Grigg MJ, Sattabongkot J, Lacerda M, Vahi V, Mazhari R, Mueller I, Longley RJ. An optimised serological machine learning model enabling targeted test-and-treat for Plasmodium vivax malaria. medRxiv 2026. https://doi.org/10.64898/2026.08.09.26355326