Estimating Infection Rates from Serological Data

Translates antibody levels measured in a (cross-sectional) population sample into an estimate of the frequency with which seroconversions (infections) occur in the sampled population.

seroincidence package

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. Formulated simply: the presence of many high titres indicates that many subjects likely experienced infection recently, while low titres indicate a low frequency of infections in the sampled population.

The seroincidence calculator script was designed to use the longitudinal response characteristics by means of a set of parameters characterizing the longitudinal response of the selected serum antibodies.


seroincidence v.2.0.0 (Release date: 2018-06-05)


  • A complete rewrite of the methodology and the implementation.

seroincidence v.1.0.5 (Release date: 2015-12-29)


  • Packages "stats" and "utils" listed in the "Imports" section of DESCRIPTION. Imported functions are called as "pkg::fun()".
  • Vignette "methodology.Rmd" made compatible with rmarkdown 0.9. Line "- \usepackage[pdftex]{graphicx}" removed.
  • Oxygen documentation made compatible with roxygen2 5.0.1. Values for tags "docType" and "news" put on the same line.

seroincidence v.1.0.4 (Release date: 2015-05-22)


  • URL for package location on ECDC website updated.

seroincidence v.1.0.3 (Release date: 2015-04-10)


  • LICENSE file removed, reference to that file removed from DESCRIPTION
  • NEWS updated
  • changed the version numbering from 1.0.2 to 1.0.3.

seroincidence v.1.0.2 (Release date: 2015-04-09)


  • manually corrected break line in URL in DESCRIPTION file in the source package "tar.gz" file (inserted there by the R build system).
  • ensured that all references to URL from DESCRIPTION (in citation, vignettes) have all break lines removed.
  • fixed one reference in the vignettes.
  • changed the version numbering from 1.0.1 to 1.0.2.

seroincidence v.1.0.1 (Release date: 2015-03-31)


  • All titles (package, functions, data sets) changed to title case
  • All S3 methods exported and registered
  • All exported functions/data sets are documented with examples including comments. Examples requiring time consuming calculations are put in \dontrun environment.

seroincidence v.1.0.0 (Release date: 2015-03-18)


  • Vignettes reformatted

seroincidence v.0.9.9 (Release date: 2015-03-04)


  • Vignette's content updated

seroincidence v.0.9.8 (Release date: 2015-02-25)


  • "Methodology" document extracted from the tutorial and converted to pdf.
  • Fixes of typos in the methodology document.
  • Fixes of typos, formatting, references, additional text in the tutorial.
  • Restructuring and additional text in the installation manual.
  • Acronym "GUI" expanded to "graphical user interface".
  • Description of parametric models in "simulateSerologyData.R", "simulateSalmonellaResponseParams" and the tutorial.
  • Description of response parameters added in the tutorial (section "Specifying longitudinal response parameters").
  • Description of outputs of the summary function in the tutorial.
  • Spell check run on the installation, tutorial and methodology.

seroincidence v.0.9.7 (Release date: 2015-01-30)


  • Tutorial vignettes customized for pdf and html output
  • Sections "Antibody decay and seroincidence" of the tutorial vignettes include now subsections on censoring and checks.

seroincidence v.0.9.6 (Release date: 2014-12-19)


  • Fix intialization of variable "progressBarCreated" in "estimateSeroincidence".
  • Added URL to ECDC website
  • "estimateSeroincidence" and "summary.seroincidence" updated: operate on output of "optim" function.
  • printing functions added for outputs of "estimateSeroincidence" and "summary.seroincidence"

Reference manual

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2.0.0 by Chantal Quinten, 8 months ago

Browse source code at

Authors: Peter Teunis [aut] (Author of the method and original code.) , Jan van Eijkeren [aut] (Author of the method and original code.) , Daniel Lewandowski [com, ctb] (Creator of the R package.) , Chantal Quinten [cre, ctb] (Project manager and the package maintainer.)

Documentation:   PDF Manual  

GPL-3 license

Imports stats, utils

Suggests knitr, rmarkdown, parallel

See at CRAN