lrs.multistate: Likelihood Ratio Statistic to Compare Embedded Multistate...

Description Usage Arguments Value Author(s) Examples

View source: R/lrs.multistate.R

Description

This function computes a Likelihood Ratio Statistic to compare two embedded multistate models.

Usage

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lrs.multistate(model1, model0)

Arguments

model1

A list containing the results after using a function included in the multistate package.

model0

A list containing the results after using a function included in the multistate package. The function used to obtained the model0 have to be the same than the one used to obtain the model1. The model0 have to be embedded in the model1.

Value

statistic

The value of the statistic.

ddl

Degrees of freedom.

pvalue

p-value.

Author(s)

Yohann Foucher <Yohann.Foucher@univ-nantes.fr> and

Florence Gillaizeau <Florence.Gillaizeau@univ-nantes.fr>

Examples

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data(dataDIVAT)

# A subgroup analysis to reduce the time needed for this example

dataDIVAT$id<-c(1:nrow(dataDIVAT))
set.seed(2)
d3<-dataDIVAT[dataDIVAT$id %in% sample(dataDIVAT$id, 250, replace = FALSE),]

# To illustrate the use of a 3-state model, individuals with trajectory 13 and 123 are 
# censored at the time of transition into state X=3

d3$trajectory[d3$trajectory==13]<-1
d3$trajectory[d3$trajectory==123]<-12
d3$trajectory[d3$trajectory==14]<-13
d3$trajectory[d3$trajectory==124]<-123

# 3-state parametric semi-Markov model : does 'z' influence both the
# transition 1->3 ? We only reduced the precision and the number of iteration
# to save time in this example, prefere the default values.

m1 <- sm3(t1=d3$time1, t2=d3$time2, sequence=d3$trajectory, dist=c("E","E","E"),
  ini.dist.12=c(9.93), ini.dist.13=c(11.54), ini.dist.23=c(10.21),
  cov.12=d3$z, init.cov.12=c(-0.13), names.12=c("beta12_z"),
  cov.13=d3$z, init.cov.13=c(1.61),  names.13=c("beta13_z"),
  conf.int=TRUE, silent=FALSE, precision=0.001)
  
m1

m0 <- sm3(t1=d3$time1, t2=d3$time2, sequence=d3$trajectory, dist=c("E","E","E"),
  ini.dist.12=c(9.93), ini.dist.13=c(11.54), ini.dist.23=c(10.21),
  cov.12=d3$z, init.cov.12=c(-0.13), names.12=c("beta12_z"),
  conf.int=TRUE, silent=FALSE, precision=0.001)

m0

lrs.multistate(model1=m1, model0=m0)

Example output

Loading required package: survival
Loading required package: statmod
Loading required package: date
Loading required package: relsurv

 ******  3-state semi-Markov model ****** 
-747.7689 
-747.7689 
-747.7689 

 Number of data rows: 250Number of data rows with missing values (deleted): 0 
$object
[1] "sm3 (3-state semi-markov model)"

$dist
[1] "E" "E" "E"

$cuts.12
NULL

$cuts.13
NULL

$cuts.23
NULL

$covariates
[1] 1 1 0

$table
                          Estimate Std.Error t.value Pr(>|t|)
1 log(sigma) on trans. 12   8.3683    0.1543 54.2339   0.0000
2 log(sigma) on trans. 13  10.4961    0.4471 23.4750   0.0000
3 log(sigma) on trans. 23  10.2164    0.5770 17.7052   0.0000
4 beta12_z                  0.2253    0.2559  0.8805   0.3786
5 beta13_z                  0.5611    0.6708  0.8364   0.4029

$cov.matrix
             [,1]         [,2]          [,3]          [,4]         [,5]
[1,] 2.380828e-02 3.381919e-10  1.126534e-10  2.380828e-02 8.459337e-10
[2,] 3.381919e-10 1.999148e-01  4.729675e-09  8.117579e-10 1.999148e-01
[3,] 1.126534e-10 4.729675e-09  3.329631e-01 -2.817145e-10 8.280105e-09
[4,] 2.380828e-02 8.117579e-10 -2.817145e-10  6.548133e-02 1.615743e-09
[5,] 8.459337e-10 1.999148e-01  8.280105e-09  1.615743e-09 4.500320e-01

$LogLik
[1] -747.7689

$AIC
[1] 1505.538


 ******  3-state semi-Markov model ****** 
-748.1084 
-748.1084 
-748.1084 

 Number of data rows: 250Number of data rows with missing values (deleted): 0 
$object
[1] "sm3 (3-state semi-markov model)"

$dist
[1] "E" "E" "E"

$cuts.12
NULL

$cuts.13
NULL

$cuts.23
NULL

$covariates
[1] 1 0 0

$table
                          Estimate Std.Error t.value Pr(>|t|)
1 log(sigma) on trans. 12   8.3682    0.1543 54.2355   0.0000
2 log(sigma) on trans. 13  10.2844    0.3333 30.8546   0.0000
3 log(sigma) on trans. 23  10.2179    0.5775 17.6946   0.0000
4 beta12_z                  0.2255    0.2559  0.8812   0.3782

$cov.matrix
              [,1]          [,2]          [,3]          [,4]
[1,]  2.380646e-02 -7.517282e-11 -1.128125e-10  2.380646e-02
[2,] -7.517282e-11  1.111004e-01 -2.672008e-19 -2.067322e-10
[3,] -1.128125e-10 -2.672008e-19  3.334589e-01  8.461978e-11
[4,]  2.380646e-02 -2.067322e-10  8.461978e-11  6.546997e-02

$LogLik
[1] -748.1084

$AIC
[1] 1504.217

statistic       ddl    pvalue 
0.6789791 1.0000000 0.4099385 

multistate documentation built on May 2, 2019, 5:16 a.m.