Epi: lines.apc – R documentation

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lines.apc

Plot APC-estimates in an APC-frame.

Description

When an APC-frame has been produced by apc.frame, this function draws a set of estimates from an APC-fit in the frame. An optional drift parameter can be added to the period parameters and subtracted from the cohort and age parameters.

Usage

## S3 method for class 'apc'
lines( x, P, C,
        scale = c("log","ln","rates","inc","RR"),
    frame.par = options()[["apc.frame.par"]],
        drift = 0,
           c0 = median( C[,1] ),
           a0 = median( A[,1] ),
           p0 = c0 + a0,
           ci = rep( FALSE, 3 ),
          lwd = c(3,1,1),
          lty = 1,
          col = "black",
         type = "l",
        knots = FALSE,
        shade = FALSE,
          ... )
 apc.lines( x, P, C,
        scale = c("log","ln","rates","inc","RR"),
    frame.par = options()[["apc.frame.par"]],
        drift = 0,
           c0 = median( C[,1] ),
           a0 = median( A[,1] ),
           p0 = c0 + a0,
           ci = rep( FALSE, 3 ),
          lwd = c(3,1,1),
          lty = 1,
          col = "black",
         type = "l",
        knots = FALSE,
        shade = FALSE,
          ... )

Arguments

`x`	If an `apc`-object, (see `apc.fit`), then the arguments `P`, `C`, `c0`, `a0` and `p0` are ignored, and the estimates from `x` plotted. Can also be a 4-column matrix with columns age, age-specific rates, lower and upper c.i., in which case period and cohort effects are taken from the arguments `P` and `C`.
`P`	Period effects. Rate-ratios. Same form as for the age-effects.
`C`	Cohort effects. Rate-ratios. Same form as for the age-effects.
`scale`	Are effects given on a log-scale? Character variable, one of `"log"`, `"ln"`, `"rates"`, `"inc"`, `"RR"`. If `"log"` or `"ln"` it is assumed that effects are log(rates) and log(RRs) otherwise the actual effects are assumed given in `A`, `P` and `C`. If `A` is of class `apc`, it is assumed to be `"rates"`.
`frame.par`	2-element vector with the cohort-period offset and RR multiplicator. This will typically be the result from the call of `apc.frame`. See this for details.
`drift`	The drift parameter to be added to the period effect. If `scale="log"` this is assumed to be on the log-scale, otherwise it is assumed to be a multiplicative factor per unit of the first columns of `A`, `P` and `C`
`c0`	The cohort where the drift is assumed to be 0; the subtracted drift effect is `drift*(C[,1]-c0)`.
`a0`	The age where the drift is assumed to be 0.
`p0`	The period where the drift is assumed to be 0.
`ci`	Should confidence interval be drawn. Logical or character. If character, any occurrence of `"a"` or `"A"` produces confidence intervals for the age-effect. Similarly for period and cohort.
`lwd`	Line widths for estimates, lower and upper confidence limits.
`lty`	Linetypes for the three effects.
`col`	Colours for the three effects.
`type`	What type of lines / points should be used.
`knots`	Should knots from the model be shown?
`shade`	Should confidence intervals be plotted as shaded areas? If true, the setting of `ci` is ignored.
`...`	Further parameters to be transmitted to `points` `lines`, `matpoints` or `matlines` used for plotting the three sets of curves.

Details

There is no difference between the functions apc.lines and lines.apc, except the the latter is the lines method for apc objects.

The drawing of three effects in an APC-frame is a rather trivial task, and the main purpose of the utility is to provide a function that easily adds the functionality of adding a drift so that several sets of lines can be easily produced in the same frame.

Value

apc.lines returns (invisibly) a list of three matrices of the effects plotted.

Author(s)

Bendix Carstensen, Steno Diabetes Center, http://bendixcarstensen.com