Introduction | Estimating MDRI using binomial regression | Example of mdrical using the complementary log-log functional form and pre-classified data | Example of mdrical using the logit cubic functional form and two independent thresholds on biomarkers | Obtaining fitting parameters for bootstrap iterations | Estimating FRR using binomial proportions with frrcal
Package: inctools 1.0.15
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:
inctools_1.0.15.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
inctools/json (API)
| # Install 'inctools' in R: |
| install.packages('inctools', repos = c('https://eduardgrebe.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).
Last updated from:164456cc42. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 142 | ||
| source / vignettes | OK | 223 | ||
| linux-release-x86_64 | OK | 139 | ||
| macos-release-arm64 | OK | 181 | ||
| macos-oldrel-arm64 | OK | 145 | ||
| windows-devel | OK | 86 | ||
| windows-release | OK | 86 | ||
| windows-oldrel | OK | 100 | ||
| wasm-release | OK | 158 |
Exports:frrcalinccountsincpowerincprecisionincpropsmdricalprevcounts
Dependencies:binomclicodetoolscpp11cubaturedoParalleldplyrfarverforeachgenericsggplot2glm2gluegmmgtableisobanditeratorslabelinglatticelifecyclemagrittrMatrixmvtnormpillarpkgconfigplyrpracmaR6RColorBrewerRcpprlangS7sandwichscalestibbletidyselecttmvtnormutf8vctrsviridisLitewithrzoo
Recent infection test calibration
Last update: 2019-11-07
Started: 2016-05-18
Overview of Incidence Estimation Package inctools
Introduction | Historical context | Overview of Functionality and Use | Analysis in support of survey design | Analysis of survey data | Estimation of key performance characteristics of Tests for Recent Infection | Glossary | HIV infected individual | Mean duration of recent infection (MDRI) | False-recent rate (FRR) | Incidence as a (or, an “instantaneous”) rate | Annual(ised) risk of infection | Recency time cut-off T (“Big T”) | Relative standard error (RSE) | Null hypothesis | p-value | Significance | Sample size | Design effect | Citation | Acknowledgements | Appendix: Technical details | Case 1: Surveys share a single estimate for MDRI and a single estimate for FRR | Case 2: Surveys share a single estimate for MDRI, but have independent FRR estimates | Case 3: Both MDRI and FRR are independently estimated in each survey | Note: | Crucial note on choice of null hypothesis, calculation of p-values and meaning of “statistical power”
Last update: 2018-09-21
Started: 2016-05-18
Estimating incidence from cross-sectional data
Introduction | Analytical Paradigm | Using functions incprops and inccounts | Examples | Function prevcounts
Last update: 2018-01-03
Started: 2016-05-18
Survey design: power, precision and sample size
Function incpower | Examples | Function incprecision
Last update: 2018-01-03
Started: 2016-05-18
