Package: inctools 1.0.9006

Eduard Grebe

inctools: Incidence Estimation Tools

Tools for estimating incidence from biomarker data in cross- sectional surveys, and for calibrating tests for recent infection. Implements and extends the method of Kassanjee et al. (2012) <doi:10.1097/EDE.0b013e3182576c07>.

Authors:Eduard Grebe [cre, aut], Alex Welte [aut], Avery McIntosh [aut], Petra Bäumler [aut], Reshma Kassanjee [ctb], Hilmarie Brand [ctb], Cari Van Schalkwyk [ctb], Yuruo Li [ctb], Simon Daniel [ctb], Stefano Ongarello [aut], Yusuke Asai [ctb], Jeffrey Eaton [ctb]

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inctools.pdf |inctools.html✨
inctools/json (API)

# Install 'inctools' in R:
install.packages('inctools', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sacema/inctools/issues

Datasets:
  • excalibdata - The dataset 'excalibdata.Rdata' contains example data from an evaluation of an assay measuring recency of infection. At an assay result of <10, the specimen is considered to be recently infected. It further contains viral load data, which is commonly used to reduce false recency. For example, when recency is defined as assay result <10 and viral load > 1000, the FRR is substantially lower (but the MDRI is also reduced).

On CRAN:

biomarkersbiostatisticsepidemiologyhivincidenceincidence-estimationincidence-inferenceinfectious-diseasesstatistics

6.51 score 6 stars 27 scripts 288 downloads 2 mentions 7 exports 51 dependencies

Last updated 4 years agofrom:4877c42d6f. Checks:1 OK, 7 NOTE. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKFeb 15 2025
R-4.5-winNOTEFeb 15 2025
R-4.5-macNOTEFeb 15 2025
R-4.5-linuxNOTEFeb 15 2025
R-4.4-winNOTEFeb 15 2025
R-4.4-macNOTEFeb 15 2025
R-4.3-winNOTEFeb 15 2025
R-4.3-macNOTEFeb 15 2025

Exports:frrcalinccountsincpowerincprecisionincpropsmdricalprevcounts

Dependencies:binomclicodetoolscolorspacecpp11cubaturedoParalleldplyrfansifarverforeachgenericsggplot2glm2gluegmmgtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigplyrpracmapurrrR6RColorBrewerRcpprlangsandwichscalesstringistringrtibbletidyrtidyselecttmvtnormutf8vctrsviridisLitewithrzoo

Estimating incidence from cross-sectional data

Rendered fromEstimatingIncidence.Rmdusingknitr::rmarkdownon Feb 15 2025.

Last update: 2021-03-29
Started: 2021-03-29

Overview of Incidence Estimation Package inctools

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Feb 15 2025.

Last update: 2021-03-29
Started: 2021-03-29

Survey design: power, precision and sample size

Rendered fromSurveyDesign.Rmdusingknitr::rmarkdownon Feb 15 2025.

Last update: 2021-03-29
Started: 2021-03-29

Recent infection test calibration

Rendered fromTestCalibration.Rmdusingknitr::rmarkdownon Feb 15 2025.

Last update: 2021-03-29
Started: 2021-03-29