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/json (API)

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

Peer review:

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 208 downloads 2 mentions 7 exports 51 dependencies

Last updated 4 years agofrom:4877c42d6f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 13 2024
R-4.5-winNOTEOct 13 2024
R-4.5-linuxNOTEOct 13 2024
R-4.4-winNOTEOct 13 2024
R-4.4-macNOTEOct 13 2024
R-4.3-winNOTEOct 13 2024
R-4.3-macNOTEOct 13 2024

Exports:frrcalinccountsincpowerincprecisionincpropsmdricalprevcounts

Dependencies:binomclicodetoolscolorspacecpp11cubaturedoParalleldplyrfansifarverforeachgenericsggplot2glm2gluegmmgtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigplyrpracmapurrrR6RColorBrewerRcpprlangsandwichscalesstringistringrtibbletidyrtidyselecttmvtnormutf8vctrsviridisLitewithrzoo

Estimating incidence from cross-sectional data

Rendered fromEstimatingIncidence.Rmdusingknitr::rmarkdownon Oct 13 2024.

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

Overview of Incidence Estimation Package inctools

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Oct 13 2024.

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

Survey design: power, precision and sample size

Rendered fromSurveyDesign.Rmdusingknitr::rmarkdownon Oct 13 2024.

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

Recent infection test calibration

Rendered fromTestCalibration.Rmdusingknitr::rmarkdownon Oct 13 2024.

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