[R] P-values Kolmogorov–Smirnov test

[Boo G.]

Thanks for your reply, Rui. 

I don’t think that I can use directly the ks.test because I have a weighted sample (see  m_2 <-m_1[(sample(nrow(m_1), size=i, prob=p_1, replace=F)),]) and I want to account for that. That’s why I am trying to compute everything manually. 

Also, if you look at the results of the ks.test in your simulation, you will notice that the p-value always implies that the sample is always (even with same size = 1) drawn form the same distribution. This looks suspicious to me.

What are your thoughts?

> 

> On 5 Sep 2019, at 20:29, Rui Barradas <ruipbarradas using sapo.pt> wrote:
> 
> Hello,
> 
> I don't have the algorithms at hand but the KS statistic calculation is more complicated than your max/abs difference.
> 
> Anyway, why not use ks.test? it's not that difficult:
> 
> 
> set.seed(1234)
> #reference distribution
> d_1 <- sort(rpois(1000, 500))
> p_1 <- d_1/sum(d_1)
> m_1 <- data.frame(d_1, p_1)
> 
> #data frame to store the values of the simulation
> d_stat <- data.frame(1:1000, NA, NA)
> names(d_stat) <- c("sample_size", "ks_distance", "p_value")
> 
> #simulation
> for (i in 1:1000) {
>  #sample from the reference distribution
>  m_2 <-m_1[(sample(nrow(m_1), size=i, prob=p_1, replace=F)),]
>  d_2 <- m_2$d_1
> 
>  ht <- ks.test(d_1, d_2)
>  #kolmogorov-smirnov distance
>  d_stat[i, 2] <- ht$statistic
>  d_stat[i, 3] <- ht$p.value
> }
> 
> hist(d_stat[, 2])
> hist(d_stat[, 3])
> 
> 
> Note that d_2 is not sorted, but the results are equal in the sense of function identical(), meaning they are *exactly* the same. Why shouldn't they?
> 
> Hope this helps,
> 
> Rui Barradas
> 
> 
> Às 17:06 de 05/09/19, Boo G. escreveu:
>> Hello,
>> I am trying to perform a Kolmogorov–Smirnov test to assess the difference between a distribution and samples drawn proportionally to size of different sizes. I managed to compute the Kolmogorov–Smirnov distance but I am lost with the p-value. I have looked into the ks.test function unsuccessfully. Can anyone help me with computing p-values for a two-tailed test?
>> Below a simplified version of my code.
>> Thanks in advance.
>> Gianluca
>> library(spatstat)
>> #reference distribution
>> d_1 <- sort(rpois(1000, 500))
>> p_1 <- d_1/sum(d_1)
>> m_1 <- data.frame(d_1, p_1)
>> #data frame to store the values of the siumation
>> d_stat <- data.frame(1:1000, NA, NA)
>> names(d_stat) <- c("sample_size", "ks_distance", "p_value")
>> #simulation
>> for (i in 1:1000) {
>>   #sample from the reference distribution
>>   m_2 <-m_1[(sample(nrow(m_1), size=i, prob=p_1, replace=F)),]
>>   m_2 <-m_2[order(m_2$d_1),]
>>   d_2 <- m_2$d_1
>>   p_2 <- m_2$p_1
>>   #weighted ecdf for the reference distribution and the sample
>>   f_d_1 <- ewcdf(d_1, normalise=F)
>>   f_d_2 <- ewcdf(d_2, 1/p_2, normalise=F, adjust=1/length(d_2))
>>   #kolmogorov-smirnov distance
>>   d_stat[i,2] <- max(abs(f_d_1(d_2) - f_d_2(d_2)))
>> }
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