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Last data update: 2014.03.03

R: Plots survival function.

plot.MSLT.S

R Documentation

Plots survival function.

Description

Plot method for object of class 'MSLT.S' using the ggplot2 package. It plots the multistate survival function by as estimated by MSLT.S

Usage

## S3 method for class 'MSLT.S'
plot(x, e0, order,colours,title,area,xmin,xmax,...)

Arguments

`x`	The multistate survival function. An object of class `MSLT.S` produced by the `MSLT.S` function. It is one of two components of the object produced by the `MSLT.S` function.
`e0`	Life expectancy at reference age (e.g. at birth)
`order`	Desired sequence of states in plot
`colours`	Colours
`title`	Title for multistate survival plot
`area`	Graph type: area (area=TRUE) or bar (area=FALSE)
`xmin`	Minimum value on x-axis
`xmax`	Maximum value on x-axis
`...`	Further arguments to plot

Value

The function plot.MSLT.S returns the multistate survival function (S) and the plot. It returns an object with the following components:

`S`	The multistate survival function (values used in the plot)
`plot`	The plot produced by the ggplot2 package.

Author(s)

Frans Willekens

Examples

   	
# The multistate life table based on occurrence-exposure rates
    data (GLHS)
    param <- Parameters (GLHS)
    cr <- Cumrates (irate=3,Bdata=GLHS)
    S <- MSLT.S(cr$oe)
    radix <- c(10000,0)
    mslt <- MSLT.e (S,radix)
    
# Plot the multistate survival function (object of class 'MSLT.S' )
    z<- plot (x=S$S,e0=mslt$e0,title="Multistate survival function",area=TRUE,order=c("N","J"))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Biograph)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Biograph/plot.MSLT.S.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.MSLT.S
> ### Title: Plots survival function.
> ### Aliases: plot.MSLT.S
> 
> ### ** Examples
>    	
> # The multistate life table based on occurrence-exposure rates
>     data (GLHS)
>     param <- Parameters (GLHS)
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
>     cr <- Cumrates (irate=3,Bdata=GLHS)
[1] ". . . . . .  Removing intrastate transitions . . . . . "
[1] . . . . . .   Removes intrastate transitions . . . .
[1] . . . . Intrastate transitions removed. Recalculating transitions . . . . 
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] A new Biograph object without intrastate transitions is returned.
[1] ". . . . . . Estimating rates . . . . ."
[1] "  "
[1] "Cumrates: calls function Biograph.mvna  . . . "
  ID born start      end    sex edu marriage LMentry  cohort path      Tr1
1  1  351     0 52.66667   Male  17      679     555 1929-31   NJ 17.00000
2  2  357     0 52.16667 Female  10      762     593 1929-31  NJN 19.66667
3  3  473     0 42.50000 Female  11      870     688 1939-41  NJN 17.91667
4  4  604     0 31.58333 Female  13      872     872 1949-51  NJN 22.33333
5  5  377     0 50.50000   Male  11      701     583 1929-31   NJ 17.16667
       Tr2 Tr3 Tr4 Tr5 Tr6 Tr7 Tr8 Tr9 Tr10 Tr11 Tr12
1       NA  NA  NA  NA  NA  NA  NA  NA   NA   NA   NA
2 44.66667  NA  NA  NA  NA  NA  NA  NA   NA   NA   NA
3 29.66667  NA  NA  NA  NA  NA  NA  NA   NA   NA   NA
4 26.91667  NA  NA  NA  NA  NA  NA  NA   NA   NA   NA
5       NA  NA  NA  NA  NA  NA  NA  NA   NA   NA   NA
[1] No intra-state transitions present in the data.
[1] "      Biograph.mvna: Calls function Biograph.long . . . "
[1] . . . . .  Creating long format  . . . . . .
[1] . . . . .  running reshape  . . . . . 
[1]  . . . . Sort data in long format  . . . . 
[1]  . . . . Adjust long format for survival package etc . . .  
[1]      Biograph.mvna completed: Object produced by Biograph.mvna: .$mvna 
[1] "Cumrates 88"
[1] ". . . . . . . . . . . . "
[1] ". . . . Running mvna . . . . . . "
[1] Computing occurrence-exposure rates
[1] Running Sequences.ind
[1] Running Occup
[1] The number of age groups is 54
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] ". . . .  Running Occup . . . . "
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] "state_time: compute state.n"
[1] Running Trans
[1] Running RateTable
[1] Running Rates
>     S <- MSLT.S(cr$oe)
>     radix <- c(10000,0)
>     mslt <- MSLT.e (S,radix)
>     
> # Plot the multistate survival function (object of class 'MSLT.S' )
>     z<- plot (x=S$S,e0=mslt$e0,title="Multistate survival function",area=TRUE,order=c("N","J"))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>