Reduce dependencies (#984)

* removing packages that I don't think get used anywhere. and removing references to fst and spss files

* Update documentation

* Update authors in description

* [check-spelling] Update metadata

Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/10469297653/attempts/1
Accepted in #984 (comment)

Signed-off-by: check-spelling-bot <[email protected]>
on-behalf-of: @check-spelling <[email protected]>

* [check-spelling] Update metadata

Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/10469690723/attempts/1https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/10469690723/attempts/1
Accepted in #984 (comment)

Signed-off-by: check-spelling-bot <[email protected]>
on-behalf-of: @check-spelling <[email protected]>

---------

Signed-off-by: check-spelling-bot <[email protected]>
Co-authored-by: marjom02 <[email protected]>
Co-authored-by: SwiftySalmon <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>

.github/actions/spelling/expect.txt

@@ -3,9 +3,10 @@ Accom
 Admissio
 admloc
 admtype
-adpe
+ADPE
 adtf
 alstr
+anomymous
 arrivalmode
 arth
 atlassian
@@ -20,12 +21,12 @@ bodyloc
 boxi
 CAK
 callr
-canx
+Canx
 carehome
 careinspectorate
 categorises
 cattend
-ccyy
+CCYY
 cdn
 cennum
 CEREBROVASC
@@ -36,10 +37,11 @@ chpstart
 cij
 Classificat
 cmh
-cnws
+CNWs
 codecov
-comhairle
+Comhairle
 commhosp
+communicty
 congen
 copd
 costinc
@@ -53,6 +55,7 @@ customise
 cvd
 dataframe
 datamart
+datas
 datazone
 datediff
 dateformat
@@ -158,7 +161,7 @@ keytime
 kis
 knitr
 lcap
-lcho
+LCHO
 lgl
 linetype
 lintr
@@ -168,9 +171,9 @@ ltd
 lubridate
 magrittr
 markdownguide
-matern
-mcbride
-mcmahon
+Matern
+mcnicol
+megan
 microsoft
 MIU
 MMMYY
@@ -203,6 +206,7 @@ parkinsons
 patflow
 pattype
 PCEC
+pcs
 PERTH
 PHIBCS
 phs
@@ -215,13 +219,15 @@ PLICS
 popluation
 Posix
 postcodes
-ppas
+Postcodesio
+PPAs
 prac
 praccode
 ptypes
 purrr
 quickstart
 rankdir
+rbindlist
 rcmdcheck
 rdd
 rdname
@@ -232,13 +238,13 @@ readr
 readxl
 reasonwait
 recid
+recordlinkage
 refailure
 reflectoring
 refsource
 reftype
 relaint
 renviron
-returnsthe
 rlang
 rmarkdown
 Rnw
@@ -268,7 +274,7 @@ simd
 slf
 slfhelper
 smr
-smra
+SMRA
 smrtype
 sourcedev
 sparra

DESCRIPTION

@@ -3,12 +3,8 @@ Title: Create the Source Linkage Files
 Version: 0.0.0.9000
 Authors@R: c(
     person("Public Health Scotland", , , "[email protected]", role = c("cre", "cph")),
+    person("Megan", "McNicol", , "[email protected]", role = "aut"),
     person("Jennifer", "Thom", , "[email protected]", role = "aut"),
-    person("James", "McMahon", , "[email protected]", role = "aut",
-           comment = c(ORCID = "0000-0002-5380-2029")),
-    person("Catherine", "Holland", , "[email protected]", role = "aut",
-           comment = c(ORCID = "0000-0002-3259-5745")),
-    person("Bateman", "McBride", , "[email protected]", role = "aut"),
     person("Zihao", "Li", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0002-5178-2124"))
   )
@@ -25,25 +21,19 @@ Imports:
     data.table (>= 1.14.6),
     dbplyr (>= 2.3.1),
     dplyr (>= 1.1.1),
-    dtplyr (>= 1.3.0),
     fs (>= 1.6.1),
-    fst (>= 0.9.8),
     future (>= 1.33.0),
     future.callr (>= 0.8.1),
-    glue (>= 1.6.2),
-    haven (>= 2.5.2),
     hms (>= 1.1.0),
     janitor (>= 2.2.0),
     keyring (>= 1.3.0),
     lubridate (>= 1.9.2),
     magrittr (>= 2.0.3),
     odbc (>= 1.3.1),
-    openssl (>= 2.0.5),
     openxlsx (>= 4.2.5),
     phsmethods (>= 0.2.2),
     phsopendata (>= 0.0.1.0),
     purrr (>= 1.0.1),
-    qs (>= 0.25.5),
     R.utils (>= 2.12.2),
     readr (>= 2.1.0),
     rlang (>= 1.1.0),

R/read_file.R

@@ -3,8 +3,6 @@
 #' @description Read a file, the function chosen to read the file is dependant
 #' on the file path.
 #'  * `.rds` uses [readr::read_rds()].
-#'  * `.fst` uses [fst::read_fst()].
-#'  * `.sav` and `.zsav` use [haven::read_spss()].
 #'  * `.csv` and `.gz` use [readr::read_csv()]. Note that this assumes any file
 #'  ending with `.gz` is a zipped CSV which isn't necessarily true!
 #'  * `.parquet` uses [arrow::read_parquet()].
@@ -19,9 +17,6 @@ read_file <- function(path, col_select = NULL, as_data_frame = TRUE, ...) {
   valid_extensions <- c(
     "rds",
     "rds.gz",
-    "fst",
-    "sav",
-    "zsav",
     "csv",
     "csv.gz",
     "parquet"
@@ -60,9 +55,6 @@ read_file <- function(path, col_select = NULL, as_data_frame = TRUE, ...) {
   data <- switch(ext,
     "rds" = readr::read_rds(file = path),
     "rds.gz" = readr::read_rds(file = path),
-    "fst" = tibble::as_tibble(fst::read_fst(path = path)),
-    "sav" = haven::read_spss(file = path, ...),
-    "zsav" = haven::read_spss(file = path, ...),
     "csv" = readr::read_csv(file = path, ..., show_col_types = FALSE),
     "csv.gz" = readr::read_csv(file = path, ..., show_col_types = FALSE),
     "parquet" = arrow::read_parquet(