CODEWITHSUNDEEP
rdistancetidyr
Nonopov
Nonopov

Reputation: 55

Calculate mean of pairwise differences between ALL observations WITHIN group() in R?

I have a table like :

Fish    Group     Position
  1       1         100
  2       1         250
  3       1         500
  4       2          25
  5       2          75
  6       2         625

I have groups of fish with their position in the stream. To know how close they are, on average, I need to calculate the mean of the difference of distances for all observations within groups.

For fish of group 1, it does:

1-2 distance = 250 - 100 = 150 
2-3 distance = 500 - 250 = 250 
3-1 distance = 500 - 100 = 400

So the mean I look for is mean(150 + 250 + 400)

The tricky thing for me is to find a way to do it in the tidyverse philosophy !

Upvotes: 1

Views: 661

Answers (1)

Duck
Duck

Reputation: 39595

If DF is your data you can try this. Hope it can help:

library(dplyr)
DF %>% group_by(Group) %>% mutate(Diff=c(last(Position)-first(Position),diff(Position)))

# A tibble: 6 x 4
# Groups:   Group [2]
   Fish Group Position  Diff
  <int> <int>    <int> <int>
1     1     1      100   400
2     2     1      250   150
3     3     1      500   250
4     4     2       25   600
5     5     2       75    50
6     6     2      625   550

As long as previous solution is just a sketch, try this modification and see if this applies for your original data:

#Create list by group
L <- split(DF,DF$Group)
#Create function
compute_d <- function(x)
{
  xv <- as.numeric(x$Position)
  y <- dist(xv)
  return(y)
}
#Apply function
lapply(L,compute_d)

The results:

$`1`
    1   2
2 150    
3 400 250

$`2`
    1   2
2  50    
3 600 550

Or even more modified (new version):

#Create list by group
L <- split(DF,DF$Group)
#Create function
compute_d <- function(x)
{
  xv <- as.numeric(x$Position)
  y <- dist(xv)
  avg <- mean(y)
  y1 <- as.data.frame(as.matrix(y))
  y2 <- cbind(x,y1)
  y2$mean <- avg
  return(y2)
}
#Apply function
z <- do.call('rbind',lapply(L,compute_d))
rownames(z)<-NULL

  Fish Group Position   1   2   3     mean
1    1     1      100   0 150 400 266.6667
2    2     1      250 150   0 250 266.6667
3    3     1      500 400 250   0 266.6667
4    4     2       25   0  50 600 400.0000
5    5     2       75  50   0 550 400.0000
6    6     2      625 600 550   0 400.0000

Upvotes: 1

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