From cde2a12c4458c1bb980abb548ee8d315269e64df Mon Sep 17 00:00:00 2001 From: MATSUNAGA Date: Tue, 8 Oct 2024 03:44:54 +0200 Subject: [PATCH 1/6] Git commit for issue #237 --- NEWS.md | 9 +++++++++ R/derive_var_afeye.R | 22 +--------------------- 2 files changed, 10 insertions(+), 21 deletions(-) diff --git a/NEWS.md b/NEWS.md index a297c28..f25a025 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,12 @@ +# admiralophtha 1.2.0. + +## Updates to Functions + +- The following function arguments of `derive_var_afeye()` are removed (#237): + + * The argument `dataset_occ` + * The argument `lat_vals` + # admiralophtha 1.1.0.9002 ## Updates to Functions diff --git a/R/derive_var_afeye.R b/R/derive_var_afeye.R index 2253b0a..f0d6e72 100644 --- a/R/derive_var_afeye.R +++ b/R/derive_var_afeye.R @@ -60,29 +60,9 @@ #' ) #' #' 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)) From 20d688db878cfd2214cd17fa55fecea1a30ef385 Mon Sep 17 00:00:00 2001 From: MATSUNAGA Date: Sun, 20 Oct 2024 14:20:26 +0200 Subject: [PATCH 2/6] Git commit for 237_deprecation_cycle --- NEWS.md | 2 +- R/derive_var_afeye.R | 2 - .../x86_64-pc-linux-gnu/47cd4c8d/KernSmooth | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/MASS | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/Matrix | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/base | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/boot | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/class | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/cluster | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/codetools | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/compiler | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/datasets | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/foreign | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/grDevices | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/graphics | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/grid | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/lattice | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/methods | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/mgcv | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nlme | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nnet | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/parallel | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/rpart | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/spatial | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/splines | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats4 | 1 + .../x86_64-pc-linux-gnu/47cd4c8d/survival | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tcltk | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tools | 1 + .../R-3.6/x86_64-pc-linux-gnu/47cd4c8d/utils | 1 + .../x86_64-pc-linux-gnu/7f990633/KernSmooth | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/MASS | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/Matrix | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/base | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/boot | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/class | 1 + .../x86_64-pc-linux-gnu/7f990633/cluster | 1 + .../x86_64-pc-linux-gnu/7f990633/codetools | 1 + .../x86_64-pc-linux-gnu/7f990633/compiler | 1 + .../x86_64-pc-linux-gnu/7f990633/datasets | 1 + .../x86_64-pc-linux-gnu/7f990633/foreign | 1 + .../x86_64-pc-linux-gnu/7f990633/grDevices | 1 + .../x86_64-pc-linux-gnu/7f990633/graphics | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/grid | 1 + .../x86_64-pc-linux-gnu/7f990633/lattice | 1 + .../x86_64-pc-linux-gnu/7f990633/methods | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/mgcv | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/nlme | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/nnet | 1 + .../x86_64-pc-linux-gnu/7f990633/parallel | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/rpart | 1 + .../x86_64-pc-linux-gnu/7f990633/spatial | 1 + .../x86_64-pc-linux-gnu/7f990633/splines | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/stats | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/stats4 | 1 + .../x86_64-pc-linux-gnu/7f990633/survival | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/tcltk | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/tools | 1 + .../R-4.1/x86_64-pc-linux-gnu/7f990633/utils | 1 + tests/testthat/test-derive_var_afeye.R | 43 ------------------- 61 files changed, 59 insertions(+), 46 deletions(-) create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/KernSmooth create mode 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renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/lattice create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/methods create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/mgcv create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nlme create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nnet create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/parallel create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/rpart create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/spatial create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/splines create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats4 create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/survival create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tcltk create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tools create mode 120000 renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/utils create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/KernSmooth create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/MASS create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/Matrix create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/base create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/boot create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/class create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/cluster create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/codetools create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/compiler create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/datasets create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/foreign create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/grDevices create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/graphics create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/grid create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/lattice create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/methods create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/mgcv create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/nlme create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/nnet create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/parallel create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/rpart create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/spatial create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/splines create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/stats create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/stats4 create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/survival create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tcltk create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tools create mode 120000 renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/utils diff --git a/NEWS.md b/NEWS.md index 7b4f215..e1ce549 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ ## Updates to Functions -- The following function arguments of `derive_var_afeye()` are removed (#237): +- 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` diff --git a/R/derive_var_afeye.R b/R/derive_var_afeye.R index f0d6e72..1eee51f 100644 --- a/R/derive_var_afeye.R +++ b/R/derive_var_afeye.R @@ -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")`. diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/KernSmooth b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/KernSmooth new file mode 120000 index 0000000..02d1517 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/KernSmooth @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/KernSmooth \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/MASS b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/MASS new file mode 120000 index 0000000..5c1ee3b --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/MASS @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/MASS \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/Matrix b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/Matrix new file mode 120000 index 0000000..29fee93 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/Matrix @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/Matrix \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/base b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/base new file mode 120000 index 0000000..e1e3cd9 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/base @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/base \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/boot b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/boot new file mode 120000 index 0000000..367a9ec --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/boot @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/boot \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/class b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/class new file mode 120000 index 0000000..0a0b1aa --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/class @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/class \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/cluster b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/cluster new file mode 120000 index 0000000..67e26c1 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/cluster @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/cluster \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/codetools b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/codetools new file mode 120000 index 0000000..2e3d5d9 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/codetools @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/codetools \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/compiler b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/compiler new file mode 120000 index 0000000..af475ad --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/compiler @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/compiler \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/datasets b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/datasets new file mode 120000 index 0000000..c7370a5 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/datasets @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/datasets \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/foreign b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/foreign new file mode 120000 index 0000000..c9024f0 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/foreign @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/foreign \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/grDevices b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/grDevices new file mode 120000 index 0000000..61ee7c8 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/grDevices @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/grDevices \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/graphics b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/graphics new file mode 120000 index 0000000..dd6945f --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/graphics @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/graphics \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/grid b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/grid new file mode 120000 index 0000000..8b14918 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/grid @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/grid \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/lattice b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/lattice new file mode 120000 index 0000000..4b65fe9 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/lattice @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/lattice \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/methods b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/methods new file mode 120000 index 0000000..84ceeaa --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/methods @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/methods \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/mgcv b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/mgcv new file mode 120000 index 0000000..67bde18 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/mgcv @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/mgcv \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nlme b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nlme new file mode 120000 index 0000000..e6b29fe --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nlme @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/nlme \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nnet b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nnet new file mode 120000 index 0000000..c7b8eda --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/nnet @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/nnet \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/parallel b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/parallel new file mode 120000 index 0000000..a3a5cae --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/parallel @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/parallel \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/rpart b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/rpart new file mode 120000 index 0000000..6e7ae66 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/rpart @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/rpart \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/spatial b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/spatial new file mode 120000 index 0000000..1543ec9 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/spatial @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/spatial \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/splines b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/splines new file mode 120000 index 0000000..12bd010 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/splines @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/splines \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats new file mode 120000 index 0000000..f595180 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/stats \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats4 b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats4 new file mode 120000 index 0000000..5054415 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/stats4 @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/stats4 \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/survival b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/survival new file mode 120000 index 0000000..f623a4d --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/survival @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/survival \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tcltk b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tcltk new file mode 120000 index 0000000..8052a2d --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tcltk @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/tcltk \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tools b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tools new file mode 120000 index 0000000..0521552 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/tools @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/tools \ No newline at end of file diff --git a/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/utils b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/utils new file mode 120000 index 0000000..877d6d4 --- /dev/null +++ b/renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/utils @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/3.6.1-0.6-gomkl-2019a/lib64/R/library/utils \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/KernSmooth b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/KernSmooth new file mode 120000 index 0000000..7fd7192 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/KernSmooth @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/KernSmooth \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/MASS b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/MASS new file mode 120000 index 0000000..667f3ff --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/MASS @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/MASS \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/Matrix b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/Matrix new file mode 120000 index 0000000..da39b82 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/Matrix @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/Matrix \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/base b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/base new file mode 120000 index 0000000..63c6b64 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/base @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/base \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/boot b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/boot new file mode 120000 index 0000000..2ed7831 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/boot @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/boot \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/class b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/class new file mode 120000 index 0000000..65975d5 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/class @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/class \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/cluster b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/cluster new file mode 120000 index 0000000..203e809 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/cluster @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/cluster \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/codetools b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/codetools new file mode 120000 index 0000000..d393dcf --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/codetools @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/codetools \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/compiler b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/compiler new file mode 120000 index 0000000..c563ccf --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/compiler @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/compiler \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/datasets b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/datasets new file mode 120000 index 0000000..c9aa00a --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/datasets @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/datasets \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/foreign b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/foreign new file mode 120000 index 0000000..30fa06b --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/foreign @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/foreign \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/grDevices b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/grDevices new file mode 120000 index 0000000..d87b47c --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/grDevices @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/grDevices \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/graphics b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/graphics new file mode 120000 index 0000000..ef6c08b --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/graphics @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/graphics \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/grid b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/grid new file mode 120000 index 0000000..ae6005d --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/grid @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/grid \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/lattice b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/lattice new file mode 120000 index 0000000..16a2df6 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/lattice @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/lattice \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/methods b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/methods new file mode 120000 index 0000000..1d6aaca --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/methods @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/methods \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/mgcv b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/mgcv new file mode 120000 index 0000000..7c13f8a --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/mgcv @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/mgcv \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/nlme b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/nlme new file mode 120000 index 0000000..bee79d2 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/nlme @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/nlme \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/nnet b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/nnet new file mode 120000 index 0000000..4c8fa43 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/nnet @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/nnet \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/parallel b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/parallel new file mode 120000 index 0000000..6d68ae0 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/parallel @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/parallel \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/rpart b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/rpart new file mode 120000 index 0000000..f04270e --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/rpart @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/rpart \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/spatial b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/spatial new file mode 120000 index 0000000..3853b3c --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/spatial @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/spatial \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/splines b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/splines new file mode 120000 index 0000000..e6f067f --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/splines @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/splines \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/stats b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/stats new file mode 120000 index 0000000..f04d6d7 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/stats @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/stats \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/stats4 b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/stats4 new file mode 120000 index 0000000..8110353 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/stats4 @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/stats4 \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/survival b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/survival new file mode 120000 index 0000000..01ff4b6 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/survival @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/survival \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tcltk b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tcltk new file mode 120000 index 0000000..3840f1e --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tcltk @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/tcltk \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tools b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tools new file mode 120000 index 0000000..e348e2a --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tools @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/tools \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/utils b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/utils new file mode 120000 index 0000000..ade39a8 --- /dev/null +++ b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/utils @@ -0,0 +1 @@ +/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/utils \ No newline at end of file diff --git a/tests/testthat/test-derive_var_afeye.R b/tests/testthat/test-derive_var_afeye.R index 5c0c65b..8e915a8 100644 --- a/tests/testthat/test-derive_var_afeye.R +++ b/tests/testthat/test-derive_var_afeye.R @@ -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" - ) -}) From c3bf5bad54ddae40bd8b29b95a99566f753a2253 Mon Sep 17 00:00:00 2001 From: MATSUNAGA Date: Sun, 20 Oct 2024 14:31:29 +0200 Subject: [PATCH 3/6] remove mis-update --- renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/KernSmooth | 1 - renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/MASS | 1 - renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/Matrix | 1 - renv/sandbox/R-3.6/x86_64-pc-linux-gnu/47cd4c8d/base | 1 - 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newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tcltk b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tcltk deleted file mode 120000 index 3840f1e..0000000 --- a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tcltk +++ /dev/null @@ -1 +0,0 @@ -/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/tcltk \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tools b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tools deleted file mode 120000 index e348e2a..0000000 --- a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/tools +++ /dev/null @@ -1 +0,0 @@ -/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/tools \ No newline at end of file diff --git a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/utils b/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/utils deleted file mode 120000 index ade39a8..0000000 --- a/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/7f990633/utils +++ /dev/null @@ -1 +0,0 @@ -/CHBS/apps/EB/software/R/4.1.0-gomkl-2019a-RAN/lib64/R/library/utils \ No newline at end of file From 2a03696022357d72126cf9efe74d49c0d644540f Mon Sep 17 00:00:00 2001 From: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> Date: Mon, 21 Oct 2024 14:26:37 +0000 Subject: [PATCH 4/6] Update NEWS.md --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index e1ce549..d40130c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ ## Updates to Functions -- The following function arguments of `derive_var_afeye()` are removed following the end of their deprecation cycle. (#237): +- 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` From a4b8ecbd97ae9a22e05311077e123dc8f077c9c9 Mon Sep 17 00:00:00 2001 From: MATSUNAGA Date: Fri, 25 Oct 2024 13:29:49 +0200 Subject: [PATCH 5/6] Git commit for #237_deprecation_cycle(styler) --- R/derive_var_afeye.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/derive_var_afeye.R b/R/derive_var_afeye.R index 1eee51f..0a5c804 100644 --- a/R/derive_var_afeye.R +++ b/R/derive_var_afeye.R @@ -58,7 +58,6 @@ #' ) #' #' derive_var_afeye(adae2, loc_var = AELOC, lat_var = AELAT, loc_vals = c("EYES", "RETINA")) - derive_var_afeye <- function(dataset, loc_var, lat_var, loc_vals = "EYE") { seye_vals <- c("LEFT", "RIGHT", "BILATERAL") From 4db9e6c039e849919b4f2eca934e2674c74e18a5 Mon Sep 17 00:00:00 2001 From: ukey1025 Date: Fri, 25 Oct 2024 21:13:34 +0900 Subject: [PATCH 6/6] Git commit for #237_deprecation_cycle --- DESCRIPTION | 2 +- man/derive_var_afeye.Rd | 17 +++-------------- 2 files changed, 4 insertions(+), 15 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e5f8376..0f0e3ea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -65,4 +65,4 @@ Encoding: UTF-8 Language: en-US LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 diff --git a/man/derive_var_afeye.Rd b/man/derive_var_afeye.Rd index 64d58d1..73e314e 100644 --- a/man/derive_var_afeye.Rd +++ b/man/derive_var_afeye.Rd @@ -4,19 +4,10 @@ \alias{derive_var_afeye} \title{Derive Affected Eye} \usage{ -derive_var_afeye( - dataset, - dataset_occ, - loc_var, - lat_var, - lat_vals, - loc_vals = "EYE" -) +derive_var_afeye(dataset, loc_var, lat_var, loc_vals = "EYE") } \arguments{ -\item{dataset}{Input dataset} - -\item{dataset_occ}{Input dataset +\item{dataset}{Input dataset \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Please use \code{dataset} instead.} @@ -24,12 +15,10 @@ derive_var_afeye( \item{lat_var}{Laterality variable} -\item{lat_vals}{\code{xxLAT}values for which \code{AFEYE} is derived +\item{loc_vals}{\code{xxLOC} values for which \code{AFEYE} is derived \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Please simply ensure \code{xxLAT} values are contained in \code{c("LEFT", "RIGHT", "BILATERAL")}.} - -\item{loc_vals}{\code{xxLOC} values for which \code{AFEYE} is derived} } \value{ The input occurrence dataset with Affected Eye (\code{AFEYE}) added.