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Closes #237: deprecation #251

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Closes #237: deprecation #251

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cde2a12
Git commit for issue #237
Oct 8, 2024
7da8c63
Merge branch 'main' into 237_deprecation_cycle@main
ukey1025 Oct 8, 2024
20d688d
Git commit for 237_deprecation_cycle
Oct 20, 2024
c3bf5ba
remove mis-update
Oct 20, 2024
2a03696
Update NEWS.md
manciniedoardo Oct 21, 2024
a4b8ecb
Git commit for #237_deprecation_cycle(styler)
Oct 25, 2024
4db9e6c
Git commit for #237_deprecation_cycle
ukey1025 Oct 25, 2024
d140450
Merge branch 'main' into 237_deprecation_cycle@main
manciniedoardo Nov 14, 2024
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11 changes: 10 additions & 1 deletion NEWS.md
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Original file line number Diff line number Diff line change
@@ -1,4 +1,13 @@
# admiralophtha 1.1.0.9006
# admiralophtha 1.2.0.

## Updates to Functions

- The following function arguments of `derive_var_afeye()` are removed following the end of their deprecation cycle (#237):

* The argument `dataset_occ`
* The argument `lat_vals`

# admiralophtha 1.1.0.

## Updates to Functions

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25 changes: 1 addition & 24 deletions R/derive_var_afeye.R
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Expand Up @@ -3,14 +3,12 @@
#' Derive Affected Eye (`AFEYE`) in occurrence datasets
#'
#' @param dataset Input dataset
#' @param dataset_occ Input dataset
#'
#' `r lifecycle::badge("deprecated")` Please use `dataset` instead.
#'
#' @param loc_var Location variable
#' @param lat_var Laterality variable
#' @param loc_vals `xxLOC` values for which `AFEYE` is derived
#' @param lat_vals `xxLAT`values for which `AFEYE` is derived
#'
#' `r lifecycle::badge("deprecated")` Please simply ensure `xxLAT` values are
#' contained in `c("LEFT", "RIGHT", "BILATERAL")`.
Expand Down Expand Up @@ -60,29 +58,8 @@
#' )
#'
#' derive_var_afeye(adae2, loc_var = AELOC, lat_var = AELAT, loc_vals = c("EYES", "RETINA"))
derive_var_afeye <- function(dataset, dataset_occ, loc_var, lat_var, lat_vals, loc_vals = "EYE") {
# BEGIN DEPRECATION
if (!missing(lat_vals)) {
deprecate_stop(
"1.1.0",
"derive_var_afeye(lat_vals = )",
details = "Please ensure your laterality values are from the
set `c('LEFT', 'RIGHT', 'BILATERAL')`"
)
}

if (!missing(dataset_occ)) {
deprecate_stop(
"1.1.0",
"derive_var_afeye(dataset_occ = )",
"derive_var_afeye(dataset = )"
)
}

# END DEPRECATION

derive_var_afeye <- function(dataset, loc_var, lat_var, loc_vals = "EYE") {
seye_vals <- c("LEFT", "RIGHT", "BILATERAL")
lat_vals <- c("LEFT", "RIGHT", "BILATERAL")

loc_var <- assert_symbol(enexpr(loc_var))
lat_var <- assert_symbol(enexpr(lat_var))
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17 changes: 3 additions & 14 deletions man/derive_var_afeye.Rd
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43 changes: 0 additions & 43 deletions tests/testthat/test-derive_var_afeye.R
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Expand Up @@ -58,46 +58,3 @@ test_that("derive_var_afeye Test 2: AFEYE is derived correctly when parsing loc_
keys = c("STUDYID", "USUBJID", "AELOC", "AELAT")
)
})

## Test 3: Deprecation of dataset_occ ----
test_that("derive_var_afeye Test 3: Deprecation of dataset_occ", {
expected_output3 <- tibble::tribble(
~STUDYID, ~USUBJID, ~STUDYEYE, ~AELOC, ~AELAT, ~AFEYE,
"XXX001", "P01", "RIGHT", "EYE", "RIGHT", "Study Eye",
"XXX001", "P01", "RIGHT", "EYE", "LEFT", "Fellow Eye",
"XXX001", "P01", "RIGHT", "", "", NA_character_,
)

expect_error(
actual_output3 <- expected_output3 %>%
select(-AFEYE) %>%
derive_var_afeye(
dataset = NULL,
dataset_occ = .,
loc_var = AELOC,
lat_var = AELAT
),
class = "lifecycle_error_deprecated"
)
})

## Test 4: Deprecation of lat_vals ----
test_that("derive_var_afeye Test 4: Deprecation of lat_vals", {
expected_output4 <- tibble::tribble(
~STUDYID, ~USUBJID, ~STUDYEYE, ~AELOC, ~AELAT, ~AFEYE,
"XXX001", "P01", "RIGHT", "EYE", "RIGHT", "Study Eye",
"XXX001", "P01", "RIGHT", "EYE", "LEFT", "Fellow Eye",
"XXX001", "P01", "RIGHT", "", "", NA_character_,
)

expect_error(
actual_output4 <- expected_output4 %>%
select(-AFEYE) %>%
derive_var_afeye(
loc_var = AELOC,
lat_var = AELAT,
lat_vals = c("LEFT", "RIGHT", "BILATERAL")
),
class = "lifecycle_error_deprecated"
)
})
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