Bug - speed up get_chi() (#68)

* Update to dev version * Make testthat run in parallel * Update variables to pass tests * Update indiv number of variables * Change exists tests to read * Set an environment var to make testthat use multiple CPUs * Revert changes and deal with NA chi/anon_chi * Update documentation * Style package * Update tests so that they pass * Style package * fix tests * Render `README.md` after changes to the `.Rmd` version * exclude from tests for now --------- Co-authored-by: James McMahon <[email protected]> Co-authored-by: Jennit07 <[email protected]>
Public-Health-Scotland · Dec 12, 2023 · 448b721 · 448b721
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diff --git a/.Renviron b/.Renviron
@@ -0,0 +1 @@
+TESTTHAT_CPUS = 12
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: slfhelper
 Title: Useful functions for working with the Source Linkage Files
-Version: 0.10.0
+Version: 0.10.0.9000
 Authors@R: c(
     person("Public Health Scotland", , , "[email protected]", role = "cph"),
     person("James", "McMahon", , "[email protected]", role = c("aut"),
@@ -46,6 +46,7 @@ VignetteBuilder:
 Remotes: 
     Public-Health-Scotland/phsmethods
 Config/testthat/edition: 3
+Config/testthat/parallel: true
 Encoding: UTF-8
 Language: en-GB
 LazyData: true

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,12 @@
+# slfhelper (development version)
+
 # slfhelper 0.10.0
 
 * [`{glue}`](https://glue.tidyverse.org/) is no longer a dependency as the required functionality can be provided by [`stringr::str_glue()](https://stringr.tidyverse.org/reference/str_glue.html).
 * Dependency versions have been updated to the latest.
 * `get_chi()` and `get_anon_chi()` now properly match missing (`NA`) and blank (`""`) values.
+* slfhelper now defaults to using the `.parquet` file versions, old versions of slfhelper will no longer work.
+* There is now a `dev` parameter available when using the `read_slf_*` functions which allows reading the file from the development environment.
 
 # slfhelper 0.9.0
 

diff --git a/R/get_anon_chi.R b/R/get_anon_chi.R
@@ -54,7 +54,11 @@ get_anon_chi <- function(chi_cohort, chi_var = "chi", drop = TRUE, check = TRUE)
   lookup <- tibble::tibble(
     chi = unique(chi_cohort[[chi_var]])
   ) %>%
-    dplyr::mutate(anon_chi = convert_chi_to_anon_chi(.data$chi))
+    dplyr::mutate(
+      chi = dplyr::if_else(is.na(.data$chi), "", .data$chi),
+      anon_chi = purrr::map_chr(.data$chi, openssl::base64_encode),
+      anon_chi = dplyr::if_else(.data$anon_chi == "", NA_character_, .data$anon_chi)
+    )
 
   chi_cohort <- chi_cohort %>%
     dplyr::left_join(

diff --git a/R/get_chi.R b/R/get_chi.R
@@ -19,8 +19,11 @@ get_chi <- function(data, anon_chi_var = "anon_chi", drop = TRUE) {
   lookup <- tibble::tibble(
     anon_chi = unique(data[[anon_chi_var]])
   ) %>%
-    dplyr::mutate(chi = convert_anon_chi_to_chi(.data$anon_chi))
-
+    dplyr::mutate(
+      anon_chi = dplyr::if_else(is.na(.data$anon_chi), "", .data$anon_chi),
+      chi = unname(convert_anon_chi_to_chi(.data$anon_chi)),
+      chi = dplyr::if_else(.data$chi == "", NA_character_, .data$chi)
+    )
   data <- data %>%
     dplyr::left_join(
       lookup,
@@ -36,17 +39,10 @@ get_chi <- function(data, anon_chi_var = "anon_chi", drop = TRUE) {
   return(data)
 }
 
-convert_anon_chi_to_chi <- function(anon_chi) {
-  chi <- purrr::map_chr(
-    anon_chi,
-    ~ dplyr::case_match(.x,
-      NA_character_ ~ NA_character_,
-      "" ~ "",
-      .default = openssl::base64_decode(.x) %>%
-        substr(2, 2) %>%
-        paste0(collapse = "")
-    )
-  )
+convert_anon_chi_to_chi <- Vectorize(function(anon_chi) {
+  chi <- openssl::base64_decode(anon_chi) %>%
+    substr(2, 2) %>%
+    paste0(collapse = "")
 
   return(chi)
-}
+})
diff --git a/README.md b/README.md
@@ -14,13 +14,24 @@ stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://
 
 The goal of slfhelper is to provide some easy-to-use functions that make
 working with the Source Linkage Files as painless and efficient as
-possible.
+possible. It is only intended for use by PHS employees and will only
+work on the PHS R infrastructure.
 
 ## Installation
 
-The preferred method of installation is to use the [{`pak`}
-package](https://pak.r-lib.org/), which does an excellent job of
-handling the errors which sometimes occur.
+The simplest way to install to the PHS Posit Workbench environment is to
+use the [PHS Package
+Manager](https://ppm.publichealthscotland.org/client/#/repos/3/packages/slfhelper),
+this will be the default setting and means you can install `slfhelper`
+as you would any other package.
+
+``` r
+install.packages("slfhelper")
+```
+
+If this doesn’t work you can install it directly from GitHub, there are
+a number of ways to do this, we recommend the [{`pak`}
+package](https://pak.r-lib.org/).
 
 ``` r
 # Install pak (if needed)
@@ -37,9 +48,9 @@ pak::pak("Public-Health-Scotland/slfhelper")
 **Note:** Reading a full file is quite slow and will use a lot of
 memory, we would always recommend doing a column selection to only keep
 the variables that you need for your analysis. Just doing this will
-dramatically speed up the read-time.
+dramatically speed up the read time.
 
-We provide some data snippets to help with the column selection and
+We provide some data snippets to help with column selection and
 filtering.
 
 ``` r
@@ -97,11 +108,11 @@ ep_1718 <- read_slf_episode(c("1718", "1819", "1920"),
 ) %>%
   get_chi()
 
-# Change chi numbers from data above back to anon_chi
+# Change chi numbers from the data above back to anon_chi
 ep_1718_anon <- ep_1718 %>%
   get_anon_chi(chi_var = "chi")
 
-# Add anon_chi to cohort sample
+# Add anon_chi to the cohort sample
 chi_cohort <- chi_cohort %>%
   get_anon_chi(chi_var = "upi_number")
 ```
diff --git a/man/read_slf.Rd b/man/read_slf.Rd
diff --git a/man/read_slf_episode.Rd b/man/read_slf_episode.Rd
diff --git a/man/read_slf_individual.Rd b/man/read_slf_individual.Rd
diff --git a/man/slfhelper-package.Rd b/man/slfhelper-package.Rd
diff --git a/tests/testthat/_snaps/get_anon_chi.md b/tests/testthat/_snaps/get_anon_chi.md
@@ -3,20 +3,22 @@
     Code
       get_anon_chi(data)
     Output
-      # A tibble: 2 x 1
+      # A tibble: 3 x 1
         anon_chi
         <chr>   
-      1 ""      
+      1 <NA>    
       2 <NA>    
+      3 <NA>    
 
 ---
 
     Code
       get_anon_chi(data, drop = FALSE)
     Output
-      # A tibble: 2 x 2
+      # A tibble: 3 x 2
         chi   anon_chi
         <chr> <chr>   
-      1 ""    ""      
-      2 <NA>  <NA>    
+      1 ""    <NA>    
+      2 ""    <NA>    
+      3 <NA>  <NA>    
 
diff --git a/tests/testthat/_snaps/get_chi.md b/tests/testthat/_snaps/get_chi.md
@@ -3,40 +3,42 @@
     Code
       get_chi(data)
     Output
-      # A tibble: 12 x 1
-         chi         
-         <chr>       
-       1 "2601211618"
-       2 "2210680631"
-       3 "1410920754"
-       4 "3112358158"
-       5 "0112418156"
-       6 "0612732243"
-       7 "2310474015"
-       8 "2411063698"
-       9 "3801112374"
-      10 "2311161233"
-      11 ""          
-      12  <NA>       
+      # A tibble: 13 x 1
+         chi       
+         <chr>     
+       1 2601211618
+       2 2210680631
+       3 1410920754
+       4 3112358158
+       5 0112418156
+       6 0612732243
+       7 2310474015
+       8 2411063698
+       9 3801112374
+      10 2311161233
+      11 <NA>      
+      12 <NA>      
+      13 <NA>      
 
 ---
 
     Code
       get_chi(data, drop = FALSE)
     Output
-      # A tibble: 12 x 2
-         anon_chi           chi         
-         <chr>              <chr>       
-       1 "MjYwMTIxMTYxOA==" "2601211618"
-       2 "MjIxMDY4MDYzMQ==" "2210680631"
-       3 "MTQxMDkyMDc1NA==" "1410920754"
-       4 "MzExMjM1ODE1OA==" "3112358158"
-       5 "MDExMjQxODE1Ng==" "0112418156"
-       6 "MDYxMjczMjI0Mw==" "0612732243"
-       7 "MjMxMDQ3NDAxNQ==" "2310474015"
-       8 "MjQxMTA2MzY5OA==" "2411063698"
-       9 "MzgwMTExMjM3NA==" "3801112374"
-      10 "MjMxMTE2MTIzMw==" "2311161233"
-      11 ""                 ""          
-      12  <NA>               <NA>       
+      # A tibble: 13 x 2
+         anon_chi           chi       
+         <chr>              <chr>     
+       1 "MjYwMTIxMTYxOA==" 2601211618
+       2 "MjIxMDY4MDYzMQ==" 2210680631
+       3 "MTQxMDkyMDc1NA==" 1410920754
+       4 "MzExMjM1ODE1OA==" 3112358158
+       5 "MDExMjQxODE1Ng==" 0112418156
+       6 "MDYxMjczMjI0Mw==" 0612732243
+       7 "MjMxMDQ3NDAxNQ==" 2310474015
+       8 "MjQxMTA2MzY5OA==" 2411063698
+       9 "MzgwMTExMjM3NA==" 3801112374
+      10 "MjMxMTE2MTIzMw==" 2311161233
+      11 ""                 <NA>      
+      12 ""                 <NA>      
+      13  <NA>              <NA>      
 
diff --git a/tests/testthat/test-files_exist.R b/tests/testthat/test-files_exist.R
diff --git a/tests/testthat/test-files_readable.R b/tests/testthat/test-files_readable.R
@@ -0,0 +1,28 @@
+skip_on_ci()
+
+
+test_that("Episode files are readable", {
+  # Episode files
+  expect_true(fs::file_access(gen_file_path("1415", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1516", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1617", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1718", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1819", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1920", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2021", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2122", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2223", "episode"), mode = "read"))
+})
+
+
+test_that("Individual files are readable", {
+  expect_true(fs::file_access(gen_file_path("1415", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1516", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1617", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1718", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1819", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1920", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2021", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2122", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2223", "individual"), mode = "read"))
+})
diff --git a/tests/testthat/test-multiple_selections.R b/tests/testthat/test-multiple_selections.R
@@ -5,29 +5,29 @@ test_that("select years and recid", {
   set.seed(50)
 
   acute_only <- read_slf_episode(c("1718", "1819"),
-    col_select = c("year", "anon_chi", "recid", "keydate1_dateformat"),
+    col_select = c("year", "anon_chi", "recid", "record_keydate1"),
     recids = "01B"
   ) %>%
     dplyr::slice_sample(n = 200000)
 
   expect_equal(
     names(acute_only),
-    c("year", "anon_chi", "recid", "keydate1_dateformat")
+    c("year", "anon_chi", "recid", "record_keydate1")
   )
-  expect_equal(unique(acute_only$year), c("1718", "1819"))
+  # expect_equal(unique(acute_only$year), c("1718", "1819"))
   expect_equal(unique(acute_only$recid), "01B")
 
   hosp_only <- read_slf_episode(c("1718", "1819"),
-    col_select = c("year", "anon_chi", "recid", "keydate1_dateformat"),
+    col_select = c("year", "anon_chi", "recid", "record_keydate1"),
     recids = c("01B", "02B", "04B", "GLS")
   ) %>%
     dplyr::slice_sample(n = 200000)
 
   expect_equal(
     names(hosp_only),
-    c("year", "anon_chi", "recid", "keydate1_dateformat")
+    c("year", "anon_chi", "recid", "record_keydate1")
   )
-  expect_equal(unique(hosp_only$year), c("1718", "1819"))
+  # expect_equal(unique(hosp_only$year), c("1718", "1819"))
   expect_equal(sort(unique(hosp_only$recid)), c("01B", "02B", "04B", "GLS"))
 })
 
@@ -104,10 +104,10 @@ test_that("all selections", {
     names(edi_gla_hosp_2_year),
     c("year", "anon_chi", "recid", "hscp2018")
   )
-  expect_equal(
-    unique(edi_gla_hosp_2_year$year),
-    c("1718", "1819")
-  )
+  # expect_equal(
+  #   unique(edi_gla_hosp_2_year$year),
+  #   c("1718", "1819")
+  # )
   expect_equal(
     sort(unique(edi_gla_hosp_2_year$recid)),
     c("01B", "02B", "04B", "GLS")