R - survdiff() output fields

Question

The question is about the output structure of survdiff() function form the 'survival' library. Namely, I have a data frame containing survival data

> dat
         ID      Time Treatment Gender Censored
    1  E002 2.7597536       IND      F        0
    2  E003 4.2710472   Control      M        0
    3  E005 1.4784394       IND      F        0
    4  E006 6.8993840   Control      F        1
    5  E008 9.5934292       IND      M        0
    6  E009 2.9897331   Control      F        0
    7  E014 1.3470226       IND      F        1
    8  E016 2.1683778   Control      F        1
    9  E018 2.7597536       IND      F        1
    10 E022 1.3798768       IND      F        0
    11 E023 0.7227926       IND      M        1
    12 E024 5.5195072       IND      F        0
    13 E025 2.4640657   Control      F        0
    14 E028 7.4579055   Control      M        1
    15 E029 5.5195072   Control      F        1
    16 E030 2.7926078       IND      M        0
    17 E031 4.9938398   Control      F        0
    18 E032 2.7268994       IND      M        0
    19 E033 0.1642710       IND      M        1
    20 E034 4.1396304   Control      F        0

and a model

> diff = survdiff(Surv(Time, Censored) ~ Treatment+Gender, data = dat)
> diff
Call:
survdiff(formula = Surv(Time, Censored) ~ Treatment + Gender, 
    data = dat)

                            N Observed Expected (O-E)^2/E (O-E)^2/V
Treatment=Control, Gender=M 2        1     1.65  0.255876  0.360905
Treatment=Control, Gender=F 7        3     2.72  0.027970  0.046119
Treatment=IND, Gender=M     5        2     2.03  0.000365  0.000519
Treatment=IND, Gender=F     6        2     1.60  0.100494  0.139041

 Chisq= 0.5  on 3 degrees of freedom, p= 0.924 

I'm wondering what's the field of the output object that contains the values from the very right column (O-E)^2/V? I'd like to use them further but can't obtain them neither from diff$obs, diff$exp, diff$var nor from their combinations.

Your help's gonna be much appreciated.

Answer 1

You can find that out in a simple way. When you just run the line "diff", you actually invoke print.survdiff(diff). You can download the package source for the survival package here, then open the archive file and in the R folder you will find a file containing this function, print.survdiff.S (you can open it with Notepad++ / Sublime / anything that can read R syntax).

As far as I can see, the last column comes from the line

((otmp-etmp)^2)/ diag(x$var)

And otmp and etmp are obtained form the object with

if (is.matrix(x$obs)){
    otmp <- apply(x$obs,1,sum)
    etmp <- apply(x$exp,1,sum)
    }
else {
    otmp <- x$obs
    etmp <- x$exp
    }

So you could obtain the same by running this code with diff instead of x (although I would advise you not to call your object diff, as that is a base function in R).