Package: incubate 1.3.0

incubate: Parametric Time-to-Event Analysis with Variable Incubation Phases

Fit parametric models for time-to-event data that show an initial 'incubation period', i.e., a variable delay phase where the hazard is zero. The delayed Weibull distribution serves as foundational data model. The specific method of 'MPSE' (maximum product of spacings estimation) and MLE-based methods are used for parameter estimation. Bootstrap confidence intervals for parameters and significance tests in a two group setting are provided.

Authors:Matthias Kuhn [aut, cre, cph]

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incubate.pdf |incubate.html✨
incubate/json (API)
NEWS

# Install 'incubate' in R:
install.packages('incubate', repos = c('https://lenz99.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://gitlab.com/imb-dev/incubate

Datasets:
  • fatigue - Small data sets from different publications
  • pollution - Small data sets from different publications
  • publication_examples - Small data sets from different publications
  • stankovic - Survival of mice with glioma under different treatments
  • susquehanna - Small data sets from different publications

On CRAN:

3.00 score 254 downloads 14 exports 23 dependencies

Last updated 3 months agofrom:1330b24007. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winOKNov 14 2024
R-4.5-linuxOKNov 14 2024
R-4.4-winOKNov 14 2024
R-4.4-macOKNov 14 2024
R-4.3-winOKNov 14 2024
R-4.3-macOKNov 14 2024

Exports:delay_modeldexp_delayeddweib_delayedmexp_delayedmweib_delayedpexp_delayedpower_diffpweib_delayedqexp_delayedqweib_delayedrexp_delayedrweib_delayedtest_difftest_GOF

Dependencies:clicodetoolsdigestfansifuturefuture.applyglobalsgluelatticelifecyclelistenvmagrittrMASSMatrixparallellypillarpkgconfigpurrrrlangsurvivaltibbleutf8vctrs

Readme and manuals

Help Manual

Help pageTopics
Format a number as percentage.as_percent
Generate bootstrap distribution of model parameters to fitted incubate model.bsDataStep
Coefficients of a delay-model fit.coef.incubate_fit
Confidence intervals for parameters of incubate-model fits.confint.incubate_fit
Fit optimal parameters according to the objective function (either MPSE or MLE-based).delay_fit
Fit a delayed Exponential or Weibull model to one or two given sample(s).delay_model
Delayed Exponential DistributionDelayedExponential dexp_delayed mexp_delayed pexp_delayed qexp_delayed rexp_delayed
Delayed Weibull DistributionDelayedWeibull dweib_delayed mweib_delayed pweib_delayed qweib_delayed rweib_delayed
Estimate rounding error based on given sample of metric values The idea is to check at which level of rounding the sample values do not change.estimRoundingError
Get delay distribution functiongetDist
Minimize an objective function with PORT routine (nlminb)minObjFunPORT
Factory method for objective function, either according to maximum product of spacings estimation ('MPSE') or according to some flavour of maximum likelihood estimation (e.g., naive ('MLEn') or corrected ('MLEc') or weighted ('MLEw') MLE).objFunFactory
Power simulation function for a two-group comparison of the delay parameter.power_diff
Small data sets from different publicationsfatigue pollution publication_examples rockette susquehanna
Calculate parameter scaling for optimization routine.scalePars
Survival of mice with glioma under different treatmentsstankovic
Test the difference for delay model parameter(s) between two uncorrelated groups, based on maximum product of spacings estimation (MPSE).test_diff
Goodness-of-fit (GOF) test statistic.test_GOF
Transform observed data to unit intervaltransform.incubate_fit
Refit an 'incubate_fit'-object with specified optimization arguments. If more things need to be changed go back to 'delay_model' and start from scratch.update.incubate_fit