nll_controls function

Negative log-likelihood function: control data only

Function returning negative log-likelihood (nll) for data in a control treatment.

nll_controls(
  a1 = a1,
  b1 = b1,
  data = data,
  time = time,
  censor = censor,
  d1 = "Weibull"
)

Arguments

• a1, b1: location and scale parameters for background mortality
• data: name of data frame containing survival data
• time: name of data frame column identifying time of event; time > 0
• censor: name of data frame column idenifying if event was death (0) or right-censoring (1)
• d1: name of probability distribution describing background mortality. Choice of; 'Weibull', 'Gumbel', 'Fréchet'; defaults to the Weibull distribution

Returns

numeric

Details

This function returns the nll based on two parameters, the location and scale parameters used to describe background mortality.

Examples

# prepare a subset of the Blanford data for analysis
  data01 <- subset(data_blanford,
    (data_blanford$block == 3) &
      (data_blanford$treatment == 'cont') &
        (data_blanford$day > 0))

# check data frame for names of columns
    head(data01)

# step #1: 'prep function' linking 'nll_controls' to data
  # and identifying parameters to estimate
    m01_prep_function <- function(a1 = a1, b1 = b1){
      nll_controls(
        a1 = a1, b1 = b1,
        data = data01,
        time = t,
        censor = censor,
        d1 = 'Weibull'
        )}

# step #2: send 'prep_function' to mle2 for maximum likelihood estimation
  # specifying starting values
    m01 <- mle2(m01_prep_function,
             start = list(a1 = 2, b1 = 0.5)
             )

    summary(m01)

See Also

nll_basic