I have vectors of time, status and gender and would like to do a Survival Analysis:
time <- c(306,455,1010,210,883,1022,310,361,218,166)
status <- c(0,1,0,1,0,0,1,0,1,1)
gender <- c("Male","Male","Female","Female","Male","Female","Female","Female","Female","Female")
A <- survfit(Surv(time, status)~gender)
Then I split the table:
library(broom)
library(dplyr)
B<-tidy(A, censored = TRUE) %>%
split(.$strata)
In that table I want certain column so I made a loop:
Time<-list()
Estimate<-list()
StdError<-list()
for (i in 1:length(B)){
Time[i] <- B[[i]][1]
Estimate[i] <- B[[i]][5]
StdError[i] <- B[[i]][6]
}
And when I try to extract and combine the column using cbind and I get this result:
result <- cbind(Time, Estimate, StdError)
>result
Time Estimate StdError
[1,] Numeric,7 Numeric,7 Numeric,7
[2,] Numeric,3 Numeric,3 Numeric,3
Can somebody explain to me why this happened and help me to fix my code so that the output would come out like this:
>result
Time Estimate StdError
[1,] 166 0.8571429 0.1543033
166 0.8571429 0.1543033
210 0.7142857 0.2390457
218 0.5714286 0.3273268
310 0.4285714 0.4364358
361 0.4285714 0.4364358
1010 0.4285714 0.4364358
1022 0.4285714 0.4364358
[2,] Time Estimate StdError
306 1.0 0.0000000
455 0.5 0.7071068
883 0.5 0.7071068
We can use lapply
lapply(B, function(x) x[c('time', 'estimate', 'std.error')])
Or without anonymous function
lapply(B, `[`, c('time', 'estimate', 'std.error'))
#$`gender=Female`
# time estimate std.error
#1 166 0.8571429 0.1543033
#2 210 0.7142857 0.2390457
#3 218 0.5714286 0.3273268
#4 310 0.4285714 0.4364358
#5 361 0.4285714 0.4364358
#6 1010 0.4285714 0.4364358
#7 1022 0.4285714 0.4364358
#$`gender=Male`
# time estimate std.error
#8 306 1.0 0.0000000
#9 455 0.5 0.7071068
#10 883 0.5 0.7071068
'Time', 'Estimate', and 'StdError' objects are list, we can cbind by looping over the elements of the list with Map
Map(cbind, Time = Time, Estimate = Estimate, StdError = StdError)
If we want to use a for loop, another option is not to create individual vectors, instead subset the dataset directly
out <- vector("list", length(B))
for(i in seq_along(B)) out[[i]] <- B[[i]][c(1, 5, 6)]