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Compactify to remove redundant archive data

Source: vignettes/compactify.Rmd
compactify.Rmd

Removing redundant update data to save space

We do not need to store version update rows that look like the last version of the corresponding observations carried forward (LOCF) for use with epiprocess‘s’ epi_archive-related functions, as they all apply LOCF to fill in data between explicit updates. By default, we even detect and remove these LOCF-redundant rows to save space; this should not impact results as long as you do not directly work with the archive’s DT field in a way that expects these rows to remain.

There are three different values that can be assigned to compactify:

  • No argument: if there are LOCF-redundant rows, removes them and issues a warning with some information about what rows were removed
  • TRUE: removes any LOCF-redundant rows without any warning or other feedback
  • FALSE: keeps any LOCF-redundant rows without any warning or other feedback

For this example, we have one chart using LOCF values, while another doesn’t use them to illustrate LOCF. Notice how the head of the first dataset differs from the second from the third value included.

library(epiprocess)
library(dplyr)

dt <- archive_cases_dv_subset$DT

locf_omitted <- as_epi_archive(dt)
#> Warning: Found rows that appear redundant based on last (version of each) observation carried forward; these rows have been removed to 'compactify' and save space:
#> Key: <geo_value, time_value, version>
#>       geo_value time_value    version percent_cli case_rate_7d_av
#>          <char>     <Date>     <Date>       <num>           <num>
#>    1:        ca 2020-06-01 2020-06-07    2.140116        6.628329
#>    2:        ca 2020-06-01 2020-06-23    2.498918        6.628329
#>    3:        ca 2020-06-01 2020-07-23    2.698157        6.603020
#>   ---                                                            
#> 4949:        tx 2021-10-18 2021-10-22          NA       23.819450
#> 4950:        tx 2021-10-19 2021-10-22          NA       24.705959
#> 4951:        tx 2021-10-20 2021-10-22          NA       16.464639
#> Built-in `epi_archive` functionality should be unaffected, but results may change if you work directly with its fields (such as `DT`). See `?as_epi_archive` for details. To silence this warning but keep compactification, you can pass `compactify=TRUE` when constructing the archive.
locf_included <- as_epi_archive(dt, compactify = FALSE)

head(locf_omitted$DT)
#> Key: <geo_value, time_value, version>
#>    geo_value time_value    version percent_cli case_rate_7d_av
#>       <char>     <Date>     <Date>       <num>           <num>
#> 1:        ca 2020-06-01 2020-06-02          NA        6.628329
#> 2:        ca 2020-06-01 2020-06-06    2.140116        6.628329
#> 3:        ca 2020-06-01 2020-06-08    2.140379        6.628329
#> 4:        ca 2020-06-01 2020-06-09    2.114430        6.628329
#> 5:        ca 2020-06-01 2020-06-10    2.133677        6.628329
#> 6:        ca 2020-06-01 2020-06-11    2.197207        6.628329
head(locf_included$DT)
#> Key: <geo_value, time_value, version>
#>    geo_value time_value    version percent_cli case_rate_7d_av
#>       <char>     <Date>     <Date>       <num>           <num>
#> 1:        ca 2020-06-01 2020-06-02          NA        6.628329
#> 2:        ca 2020-06-01 2020-06-06    2.140116        6.628329
#> 3:        ca 2020-06-01 2020-06-07    2.140116        6.628329
#> 4:        ca 2020-06-01 2020-06-08    2.140379        6.628329
#> 5:        ca 2020-06-01 2020-06-09    2.114430        6.628329
#> 6:        ca 2020-06-01 2020-06-10    2.133677        6.628329

LOCF-redundant values can mar the performance of dataset operations. As the column case_rate_7d_av has many more LOCF-redundant values than percent_cli, we will omit the percent_cli column for comparing performance.

dt2 <- select(dt, -percent_cli)

locf_included_2 <- as_epi_archive(dt2, compactify = FALSE)
locf_omitted_2 <- as_epi_archive(dt2, compactify = TRUE)

In this example, a huge proportion of the original version update data were LOCF-redundant, and compactifying saves a large amount of space. The proportion of data that is LOCF-redundant can vary widely between data sets, so we won’t always be this lucky.

nrow(locf_included_2$DT)
#> [1] 129638
nrow(locf_omitted_2$DT)
#> [1] 9055

As we would expect, performing 1000 iterations of dplyr::filter is faster when the LOCF values are omitted.

# Performance of filtering
iterate_filter <- function(my_ea) {
  for (i in 1:1000) {
    filter(my_ea$DT, version >= as.Date("2020-01-01") + i)
  }
}

elapsed_time <- function(fx) c(system.time(fx))[[3]]

speed_test <- function(f, name) {
  data.frame(
    operation = name,
    locf = elapsed_time(f(locf_included_2)),
    no_locf = elapsed_time(f(locf_omitted_2))
  )
}

speeds <- speed_test(iterate_filter, "filter_1000x")

We would also like to measure the speed of epi_archive methods.

# Performance of as_of iterated 200 times
iterate_as_of <- function(my_ea) {
  for (i in 1:1000) {
    my_ea %>% epix_as_of(min(my_ea$DT$time_value) + i - 1000)
  }
}

speeds <- rbind(speeds, speed_test(iterate_as_of, "as_of_1000x"))

# Performance of slide
slide_median <- function(my_ea) {
  my_ea %>% epix_slide(median = median(.data$case_rate_7d_av), .before = 7)
}

speeds <- rbind(speeds, speed_test(slide_median, "slide_median"))

Here is a detailed performance comparison:

speeds_tidy <- tidyr::gather(speeds, key = "is_locf", value = "time_in_s", locf, no_locf)

library(ggplot2)

ggplot(speeds_tidy) +
  geom_bar(aes(x = is_locf, y = time_in_s, fill = operation), stat = "identity")