Plots cumulative transition rates

Description

Plots cumulative transition rates by origin, destination, and age estimated by Cumrates. The required input data are provided by the Cumrates function.

Usage

## S3 method for class 'cumrates'
plot(x,ptrans,title,...)

Arguments

Details

The function plots cumulative transition rates (cumulative hazard rates). If irate = 1 or irate = 3 it plots the Nelson-Aalen estimator at each birthday and adds lower and upper confidence intervals. If irate = 2 or irate = 3, it plots the cumulative occurrence-exposure rates. If irate = 3, the function plots both the Nelson-Aalen estimator (with confidence intervals) and the cumulative occurrence-exposure rate. The variable irate is an argument of the Cumrates function and included in the object produced by Cumrates.

Author(s)

Frans Willekens

Examples

    data(GLHS)
    Bdata.a <- date_b (GLHS,format.out="age",covs=c("marriage","LMentry"))
    cumrates <- Cumrates (irate = 3,Bdata=Bdata.a)
    z<- plot (x=cumrates,ptrans=c("NJ","JN")) 
  

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.cumrates.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.cumrates
> ### Title: Plots cumulative transition rates
> ### Aliases: plot.cumrates
> 
> ### ** Examples
> 
>     data(GLHS)
>     Bdata.a <- date_b (GLHS,format.out="age",covs=c("marriage","LMentry"))
cmc_as_age: negative ages are replaced by NA
>     cumrates <- Cumrates (irate = 3,Bdata=Bdata.a)
[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 27.33333 17.00000 1929-31   NJ 17.00000
2  2  357     0 52.16667 Female  10 33.75000 19.66667 1929-31  NJN 19.66667
3  3  473     0 42.50000 Female  11 33.08333 17.91667 1939-41  NJN 17.91667
4  4  604     0 31.58333 Female  13 22.33333 22.33333 1949-51  NJN 22.33333
5  5  377     0 50.50000   Male  11 27.00000 17.16667 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
>     z<- plot (x=cumrates,ptrans=c("NJ","JN")) 
[1] "No plot of Nelson-Aalen estimator since the computation of the estimator was skipped."
[1] 1
[1] 2
>   
> 
> 
> 
> 
> dev.off()
null device 
          1 
>