Referencing the value in the output

I'm new to r, so I'm sorry if this answer is listed elsewhere. I searched as best I could with limited knowledge of what to look for.

I am running a fragility survival analysis simulation using a perfume function and I want to run it multiple times while averaging one of the outputs. I figured out how to reference the values ​​in the outputs in all my other functions (using something like $ coef ["group", "coef"] summary (output)), which doesn't seem to work for this in any way I decided to try. I have listed the result below, the number I am trying to set is 2.076 in the output below (bottom line of output next to "gp2").

>frail1

Frailty distribution: inverse Gaussian 
Baseline hazard distribution: Weibull 
Loglikelihood: -90.577 

       ESTIMATE SE    p-val    
theta  0.043    0.524          
rho    1.185    0.228          
lambda 0.162    0.046          
gp2    2.076    0.423  0  

      

I tried

> names(frail1)
NULL


> coef(frail1)
Error: $ operator is invalid for atomic vectors


> names(summary(frail1))
NULL


> summary(frail1)$coefficients
Error in summary(frail1)$coefficients :
  $ operator is invalid for atomic vectors

      

obviously out of luck. I have listed the attributes below as this is what I have used in the past to find how to reference something. I have also listed a simplified version of the code I am using below. The result is the result.

> attributes(frail1)
$dim
[1] 4 3

$dimnames
$dimnames[[1]]
[1] "theta"  "rho"    "lambda" "gp2"   

$dimnames[[2]]
[1] "ESTIMATE" "SE"       "p-val"   


$class
[1] "parfm"  "matrix"

$call
parfm(formula = Surv(time, event) ~ gp, cluster = "id", data = d1, 
    dist = "weibull", frailty = "ingau")

$convergence
[1] 0

$it
function 
      84 

$extime
user.self 
    13.69 

$nobs
[1] 100

$shared
[1] FALSE

$loglik
[1] -67.13683

$dist
[1] "weibull"

$dq
[1] 56

$frailty
[1] "ingau"

$clustname
[1] "id"

$correct
[1] 0

$formula
[1] "Surv(time, event) ~ gp"

$terms
[1] "gp"

      

Simulation code

library(cmprsk)
library(statmod)
library(parfm)

set.seed(0)

shp <- 1 #weibull shape parameter
ns1 <- 50  #group 1 sample size
ns2 <- ns1 #group 2 sample size
hr11 <- 1 #group 1 hazard
hr21 <- 2 #group 2 hazard
frl <- 1 #frailty
alpha1 <- 2
nsim <- 1 #number of simulations


frail <- matrix(1,nsim,1)


id <- seq(1,ns1+ns2)

if(frl==1){
g1et <- matrix(rweibull(ns1,shape=shp,scale=1/(hr11*rinvgauss(1,1,alpha1))),ns1,1)
} else {
g1et <- matrix(rweibull(ns1,shape=shp,scale=1/hr11),ns1,1)
}
g2et <- matrix(rweibull(ns2,shape=shp,scale=1/hr21),ns2,1)


time <- c(g1et,g2et)


gp <- factor(c(matrix(1,ns1,1),matrix(2,ns2,1)),1:2,c(1,2)) #create treatment groups

event <- matrix(round(runif(ns1+ns2,0,1),0),ns1+ns2,1) #select first event type

d1 <- data.frame(id,gp,time,event)

frail1 <- parfm(Surv(time,event)~gp, cluster="id", data=d1, dist="weibull", frailty = "ingau")

frail1

      

Any help is greatly appreciated!

+3


source to share


1 answer


First look at frail1 with str

. Instead of being a list, it is actually a matrix

str(frail1)
 parfm [1:4, 1:3] 0.043 1.185 0.162 2.076 0.524 ...
- attr(*, "dimnames")=List of 2
  ..$ : chr [1:4] "theta" "rho" "lambda" "gp2"
  ..$ : chr [1:3] "ESTIMATE" "SE" "p-val"
snipped all the rather long list of attributes

      



So, you just link to it with [

:

  > frail1[4,1]
  #[1] 2.076003

      

+3


source







All Articles