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

# Parametric Time-to-Event Analysis with Variable Incubation Phases

## Documentation for package ‘incubate’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

as_percent | Format a number as percentage.
bsDataStep | Generate bootstrap distribution of model parameters to a fitted incubate model
buildControl | Build control list for 'delay_model()' and 'objFunFactory()'
buildDist | Builds the distribution object
coef.incubate_fit | Coefficients of a delay-model fit.
confint.incubate_fit | Confidence intervals for parameters of delay model fit
DelayedExponential | Delayed Exponential Distribution
DelayedWeibull | Delayed Weibull Distribution
delay_fit | Fit optimal parameters according to the objective function (either MPSE or MLE-based)
delay_model | Fit a delayed Exponential or Weibull model to one or two given sample(s)
dexp_delayed | Delayed Exponential Distribution
dweib_delayed | Delayed Weibull Distribution
estimRoundingError | 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.
fatigue | Small data sets from miscellaneous publications
getDist | Get delay distribution function
getVariance | Get the standard deviation of the fitted delay model fit
graphite | Small data sets from miscellaneous publications
lines.incubate_fit | Add a line fit to a plot of (another) 'incubate_fit' object
logLik.incubate_fit | Extract Log-Likelihood
long2017 | Relapse-free survival of melanoma patients under adjuvant treatment
measles_sailer | Serial interval times for measles during a long journey on a sailing vessel
mexp_delayed | Delayed Exponential Distribution
minObjFunAlt | Minimize an objective function with alternative optimizer
mweib_delayed | Delayed Weibull Distribution
near | Checks if arguments are numerically close.
objFunFactory | Factory method for objective function
pexp_delayed | Delayed Exponential Distribution
plot.incubate_fit | Plot a fitted delay-model object of class 'incubate_fit'
pollution | Small data sets from miscellaneous publications
power_diff | Power simulation function for a two-group comparison
prepResponseVar | Check and prepare the survival response(s)
pweib_delayed | Delayed Weibull Distribution
qexp_delayed | Delayed Exponential Distribution
qweib_delayed | Delayed Weibull Distribution
rexp_delayed | Delayed Exponential Distribution
rockette | Small data sets from miscellaneous publications
rockette74 | Small data sets from miscellaneous publications
rweib_delayed | Delayed Weibull Distribution
scalePars | Calculate parameter scaling for optimization routine.
stankovic | Survival time of mice with glioma under different treatments
susquehanna | Small data sets from miscellaneous publications
test_diff | Test the difference for model parameter(s) between two uncorrelated groups
test_GOF | Goodness-of-fit (GOF) test statistic (experimental!)
transform.incubate_fit | Transform observed data to unit interval
update.incubate_fit | Refit an 'incubate_fit'-object with specified optimization arguments
w1Fint | Internal MLEw-weight W1 function according to sampling distribution Weight W1 for given sample sizes (of one group). For small 'nObs' we use direct results from Monte-Carlo simulation. For higher 'nObs' we use an approximation (based on Wilson-Hilferty transformation).
w2Fint | Internal MLEw weight function W2 according to sampling distribution W2 is either taken directly from the MCSS-results (if available) or are taken from the smooth approximation function, otherwise.
w3FFint | Internal factory method for W3-function based on sampling distribution