R: Censored Poisson Family Function

cens.poisson {VGAM} | R Documentation

## Censored Poisson Family Function

### Description

Family function for a censored Poisson response.

### Usage

    cens.poisson(link = "loge", imu = NULL)

### Arguments

`link` | Link function applied to the mean; see `Links` for more choices.
`imu` | Optional initial value; see `CommonVGAMffArguments` for more information.

### Details

Often a table of Poisson counts has an entry J+ meaning >= J. This family function is similar to `poissonff` but handles such censored data. The input requires `SurvS4`. Only a univariate response is allowed. The Newton-Raphson algorithm is used.

### Value

An object of class `"vglmff"` (see `vglmff-class`). The object is used by modelling functions such as `vglm` and `vgam`.

### Warning

As the response is discrete, care is required with `Surv`, especially with `"interval"` censored data because of the `(start, end]` format. See the examples below. The examples have `y < L` as left censored and `y >= U` (formatted as `U+`) as right censored observations, therefore `L <= y < U` is for uncensored and/or interval censored observations. Consequently the input must be tweaked to conform to the `(start, end]` format.

### Note

The function `poissonff` should be used when there are no censored observations. Also, `NA`s are not permitted with `SurvS4`, nor is `type = "counting"`.

### Author(s)

Thomas W. Yee

### References

See survival for background.

### See Also

`SurvS4`, `poissonff`, `Links`.

### Examples

    # Example 1: right censored data
    set.seed(123); U <- 20
    cdata <- data.frame(y = rpois(N <- 100, exp(3)))
    cdata <- transform(cdata, cy = pmin(U, y),
                              rcensored = (y >= U))
    cdata <- transform(cdata, status = ifelse(rcensored, 0, 1))
    with(cdata, table(cy))
    with(cdata, table(rcensored))
    with(cdata, table(ii <- print(SurvS4(cy, status))))  # Check; U+ means >= U
    fit <- vglm(SurvS4(cy, status) ~ 1, cens.poisson, data = cdata, trace = TRUE)
    coef(fit, matrix = TRUE)
    table(print(depvar(fit)))  # Another check; U+ means >= U

    # Example 2: left censored data
    L <- 15
    cdata <- transform(cdata,
                       cY = pmax(L, y),
                       lcensored = y <  L)  # Note y < L, not cY == L or y <= L
    cdata <- transform(cdata, status = ifelse(lcensored, 0, 1))
    with(cdata, table(cY))
    with(cdata, table(lcensored))
    with(cdata, table(ii <- print(SurvS4(cY, status, type = "left"))))  # Check
    fit <- vglm(SurvS4(cY, status, type = "left") ~ 1, cens.poisson,
                data = cdata, trace = TRUE)
    coef(fit, matrix = TRUE)

    # Example 3: interval censored data
    cdata <- transform(cdata, Lvec = rep(L, len = N),
                              Uvec = rep(U, len = N))
    cdata <-
      transform(cdata,
                icensored = Lvec <= y & y < Uvec)  # Not lcensored or rcensored
    with(cdata, table(icensored))
    cdata <- transform(cdata, status = rep(3, N))  # 3 means interval censored
    cdata <-
      transform(cdata,
                status = ifelse(rcensored, 0, status))  # 0 means right censored
    cdata <-
      transform(cdata,
                status = ifelse(lcensored, 2, status))  # 2 means left  censored
    # Have to adjust Lvec and Uvec because of the (start, end] format:
    cdata$Lvec[with(cdata, icensored)] <- cdata$Lvec[with(cdata, icensored)] - 1
    cdata$Uvec[with(cdata, icensored)] <- cdata$Uvec[with(cdata, icensored)] - 1
    # Unchanged:
    cdata$Lvec[with(cdata, lcensored)] <- cdata$Lvec[with(cdata, lcensored)]
    cdata$Lvec[with(cdata, rcensored)] <- cdata$Uvec[with(cdata, rcensored)]
    with(cdata,
         table(ii <- print(SurvS4(Lvec, Uvec, status, type = "interval"))))  # Check

    fit <- vglm(SurvS4(Lvec, Uvec, status, type = "interval") ~ 1,
                cens.poisson, data = cdata, trace = TRUE)
    coef(fit, matrix = TRUE)
    table(print(depvar(fit)))  # Another check

    # Example 4: Add in some uncensored observations
    index <- (1:N)[with(cdata, icensored)]
    index <- head(index, 4)
    cdata$status[index] <- 1  # actual or uncensored value
    cdata$Lvec[index] <- cdata$y[index]
    with(cdata, table(ii <- print(SurvS4(Lvec, Uvec, status,
                                         type = "interval"))))  # Check

    fit <- vglm(SurvS4(Lvec, Uvec, status, type = "interval") ~ 1,
                cens.poisson, data = cdata, trace = TRUE, crit = "c")
    coef(fit, matrix = TRUE)
    table(print(depvar(fit)))  # Another check

[Package VGAM version 1.0-3 Index]