In Moohan/slfhelper: Useful functions for working with the Source Linkage Files

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Using Parquet files with the arrow package

The SLFs are available in parquet format. The {arrow} package gives some extra features which can speed up and reduce memory usage even further. You can read only specific columns read_parquet(file, col_select = c(var1, var2)).

Using arrow's 'Arrow Table' feature, you can speed up analysis efficiently. To do this, specify as_data_frame = FALSE when using SLFhelper and dplyr::collect() to read the data.

For example:

Imagine a scenario of analysing planned and unplanned beddays in Scotland, there are two ways to read the episode files and do analysis by setting as_data_frame to be TRUE or FALSE as follows.

library(slfhelper)

## FAST METHOD
# Filter for year of interest
slf_extract1 <- read_slf_episode(c("1819", "1920"),
  # Select recids of interest
  recids = c("01B", "GLS", "04B"),
  # Select columns
  col_select = c(
    "year", "anon_chi", "recid",
    "yearstay", "age", "cij_pattype"
  ),
  # return an arrow table
  as_data_frame = FALSE
) %>%
  # Filter for non-elective and elective episodes
  dplyr::filter(cij_pattype == "Non-Elective" | cij_pattype == "Elective") %>%
  # Group by year and cij_pattype for analysis
  dplyr::group_by(year, cij_pattype) %>%
  # summarise bedday totals
  dplyr::summarise(beddays = sum(yearstay)) %>%
  # collect the arrow table
  dplyr::collect()

## SLOW and DEFAULT Method
# Filter for year of interest
slf_extract2 <- read_slf_episode(c("1819", "1920"),
  # Select recids of interest
  recids = c("01B", "GLS", "04B"),
  # Select columns
  col_select = c(
    "year", "anon_chi", "recid",
    "yearstay", "age", "cij_pattype"
  ),
  # return an arrow table
  as_data_frame = TRUE # which is default
) %>%
  # Filter for non-elective and elective episodes
  dplyr::filter(cij_pattype == "Non-Elective" | cij_pattype == "Elective") %>%
  # Group by year and cij_pattype for analysis
  dplyr::group_by(year, cij_pattype) %>%
  # summarise bedday totals
  dplyr::summarise(beddays = sum(yearstay))

By specifying as_data_frame = FALSE when using reading SLF functions, one enjoys great advantages of parquet files. One of the advantages is fast query processing by reading only the necessary columns rather than entire rows. The table below demonstrates the huge impact of those advantages.

| | Time consumption (seconds) | Memory usage (MiB) | |-------------------------|:--------------------------:|:------------------:| | as_data_frame = TRUE | 4.46 | 553 | | as_data_frame = FALSE | 1.82 | 0.43 |

: Comparison of different ways of reading SLF files

Moohan/slfhelper documentation built on Feb. 1, 2025, 6:43 p.m.