q.rates {fracprolif}

Estimate Quiescence-Growth Model Rates

Description

Given an mle estimate of the distribution parameters transform into rates of growth and quiescence. The transformation into a growth rate is the exact method of Powell. The quiescence rate uses Poisson estimation. Standard errors are computed using the numerical delta method.

Usage

q.rates(dist, est)

Arguments

dist

This distribution to use for estimation, e.g. "emg" or "norm"

est

An object of class mle-class containing distribution estimates.

Value

An object of class q_rate containing (d) the growth rate and (q) the quiescence rate as a numeric vector, as well as additional attributes of stderr, n and df used.

Author(s)

Darren Tyson, Shawn Garbett

References

The method of determining growth rate is taken from POWELL E.0. (1956). Growth Rate and Generation Time of Bacteria, with Special Reference to Continuous Culture. J.Gen.Microbial V15,492-511. This makes a robust estimator in the presence of skewed distributions.

See Also

mle-class q.mle.norm.estimate q.mle.emg.estimate qsurvival.nllik

Examples

  data(ca1d.erlotinib)
  mitotic.lifespans <-
    subset(ca1d.erlotinib, !End.of.Expt & 
                           !Death        & 
                           !is.na(Lifespan))$Lifespan
  censored.lifespans <- 
    subset(ca1d.erlotinib, End.of.Expt  & 
                           !Death        & 
                           !is.na(Lifespan))$Lifespan
  r <- q.rates("emg", q.mle.emg.estimate(mitotic.lifespans, censored.lifespans))
  
  summary(r)
  
  r['d'] # Rate of division
  r['q'] # Rate of quiescense