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I have a data.frame of people broken into households where I have a set of mostly unique keys (for household, and then person within household), but sometimes it looks like 2 (or possibly more) households were given the same key.

small_example <- tibble::tribble(
  ~hh_id, ~per_id, ~ref,
  1,       1,       "a",
  1,       2,       "b",
  1,       3,       "c",
  2,       1,       "d",
  2,       1,       "e",
  2,       2,       "f",
  2,       2,       "g",
  2,       3,       "h",
  2,       4,       "i"
)

In this example, the first household is ok, but I want to split the second into 2 households randomly, but to preserve as much of the original structure as possible. In particular, I want persons "d" and "f" to stay together and "e"/"g" to stay together and then persons "h" and "i" to be added to one of these 2 households.

Here's my first attempt at this, but my code is pretty slow. I can tell I'm over-using the tidyverse, but am not sure what a better alternative is.

library(dplyr)
library(purrr)
assign_extra_id <- function(per_grp_id) {
  all_pers_df <- data_frame(orig_id = per_grp_id) %>%
    group_by(orig_id) %>%
    mutate(order_num = row_number(), total_num = n())

  max_dup_pers <- max(all_pers_df$total_num)

  if (max_dup_pers == 1) return(1)
  multi_pos_order <- accumulate(
    seq(max_dup_pers, 2, -1),
    ~sample(.x, .y - 1),
    .init = sample(seq_len(max_dup_pers), max_dup_pers)
  ) %>%
    set_names(seq(max_dup_pers, 1, -1)) %>%
    map_df(~data_frame(order_num = seq_along(.), new_id = .), .id = "total_num") %>%
    mutate(total_num = as.numeric(total_num))

  out <- left_join(all_pers_df, multi_pos_order, by = c("total_num", "order_num"))
  out$new_id
}

small_example %>%
  group_by(hh_id) %>%
  mutate(extra_id = assign_extra_id(per_id))

#> # A tibble: 9 x 4
#> # Groups:   hh_id [2]
#> hh_id per_id   ref extra_id
#> <dbl>  <dbl> <chr>    <dbl>
#> 1     1      1     a        1
#> 2     1      2     b        1
#> 3     1      3     c        1
#> 4     2      1     d        2
#> 5     2      1     e        1
#> 6     2      2     f        2
#> 7     2      2     g        1
#> 8     2      3     h        1
#> 9     2      4     i        1

And here's a timing:

bigger_example <- map_df(seq_len(100), ~mutate(small_example, hh_id = hh_id + (2 * .)))

microbenchmark::microbenchmark(
  my_attempt = bigger_example %>%
    group_by(hh_id) %>%
    mutate(extra_id = assign_extra_id(per_id)),
  times = 10
)

Unit: seconds
       expr      min       lq     mean   median       uq      max neval
 my_attempt 2.297449 2.305819 2.327998 2.312012 2.354128 2.381427    10

I want to randomly sample from the 4 sets of households I consider valid for what is currently hh_id = 2:

Set 1: hh1 = d, f, h, i;   hh2 = e, g
Set 2: hh1 = d, f;         hh2 = e, g, h, i
Set 3: hh1 = e, g;         hh2 = d, f, h, i
Set 4: hh1 = e, g, h, i;   hh2 = d, f

The logic for this when there are 3 households with the same hh_id gets even more complicated, because if there's only 1 person with a given person id, I want to sample from the households that were available when there were 2 (and so on). This is why there's the kind of hairy purrr::accumulate call.

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Yes, I think it is better to use efficient base functions for this kind of task. I'm assuming your ids are sorted so that duplicates will always be next to each other, is that right? In that case, a first idea would be to use the duplicated function. Using your example, see that:

x <- c(1, 1, 2, 2, 3, 4)
duplicated(x)
# [1] FALSE  TRUE FALSE  TRUE FALSE FALSE
1 + duplicated(x)
# [1] 1 2 1 2 1 1

However, this will not work in your more general case where there may be more than 2 duplicated households:

x <- c(1, 1, 1, 2, 2, 2, 3, 3, 4, 5)
1 + duplicated(x)
# [1] 1 2 2 1 2 2 1 2 1 1

For the general case, I would use run length encoding functions:

rle(x)
# Run Length Encoding
#   lengths: int [1:5] 3 3 2 1 1
#   values : num [1:5] 1 2 3 4 5
sequence(rle(x)$lengths)
# [1] 1 2 3 1 2 3 1 2 1 1

So I would suggest you replace your assign_extra_id with the following:

assign_extra_id2 <- function(x) sequence(rle(x)$lengths)

Update

Taking into account the added details (in the comments and updated question), maybe this function will do?

assign_extra_id3 <- function(x) {
   resample <- function(x, ...) x[sample.int(length(x), ...)]
   z <- rle(rle(x)$lengths)
   s <- sample(z$values[1])
   i <- Map(function(l,v) rep(resample(s[1:v]),l), z$lengths, z$values)
   unlist(i, use.names = FALSE)
}

It's (still) a nice speedup:

# Unit: milliseconds
#        expr        min         lq       mean    median         uq       max neval
 # op_attempt 5013.47742 5051.44837 6198.35973 5535.9724 6951.75439 9843.3606    10
 # fd_attempt   54.48751   59.92706   73.31207   62.1226   82.82826  130.2046    10
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  • \$\begingroup\$ Thanks for taking a look, this is interesting - I hadn't seen rle before. However, this isn't what I want - this is equivalent to `bigger_example %>% group_by(hh_id, per_id) %>% mutate(extra_id = row_number()). However, I want a random sample of the 4 households I consider valid. I'll try to update my question to make it clearer. \$\endgroup\$ – GregF Dec 10 '17 at 21:37
  • \$\begingroup\$ @GregF, can you please try assign_extra_id3 <- function(x) unlist(Map(function(z) sample(length(z)), split(x, x)), use.names = FALSE) \$\endgroup\$ – flodel Dec 10 '17 at 22:41
  • \$\begingroup\$ no, that's still not quite right. It doesn't keep person d/f and e/g together. set.seed(123); test <- small_example %>% group_by(hh_id) %>% mutate(extra_id = assign_extra_id3(per_id)); test$extra_id[test$ref %in% c("d", "f")] gives 2, 1 but I want them to always get the same household. \$\endgroup\$ – GregF Dec 11 '17 at 15:02
  • \$\begingroup\$ @GregF. Ok... One more try... See if my updated answer does the job? \$\endgroup\$ – flodel Dec 12 '17 at 0:54

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