fix error from cmd check

ready4-dev · Nov 15, 2023 · 81779f1 · 81779f1
1 parent 945d26b
commit 81779f1
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diff --git a/CITATION.cff b/CITATION.cff
@@ -1,12 +1,12 @@
 cff-version: 1.2.0
 message: "Matthew P Hamilton  (2023). ready4: Implement Transparent, Reusable and Updatable Computational Health
-Economic Models. Version 0.0.0.9131. Zenodo. https://doi.org/10.5281/zenodo.5606250"
+Economic Models. Version 0.0.0.9132. Zenodo. https://doi.org/10.5281/zenodo.5606250"
 authors:
   - family-names: "Hamilton"
     given-names: "Matthew P"
 title: "ready4: Implement Transparent, Reusable and Updatable Computational Health
 Economic Models"
-version: 0.0.0.9131
+version: 0.0.0.9132
 doi: 10.5281/zenodo.5606250
 date-released: 2023-11-15
 url: "https://ready4-dev.github.io/ready4/"
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -31,8 +31,6 @@ Collate:
     'C4_Ready4Module.R'
     'C4_Ready4Private.R'
     'C4_Ready4Public.R'
-    'add.R'
-    'bind.R'
     'fn_add.R'
     'fn_bind.R'
     'fn_get.R'
@@ -43,11 +41,9 @@ Collate:
     'fn_transform.R'
     'fn_update.R'
     'fn_write.R'
-    'get.R'
     'grp_generics.R'
     'imp_fns.R'
     'imp_mthds.R'
-    'make.R'
     'mthd_authorSlot.R'
     'mthd_characterizeSlot.R'
     'mthd_depictSlot.R'
@@ -64,13 +60,7 @@ Collate:
     'mthd_renewSlot.R'
     'mthd_shareSlot.R'
     'pkg_ready4.R'
-    'print.R'
     'ready4-package.R'
-    'remove.R'
-    'rowbind.R'
-    'transform.R'
-    'update.R'
-    'write.R'
 Imports: 
     assertthat,
     bib2df,
@@ -80,7 +70,6 @@ Imports:
     fs,
     Hmisc,
     kableExtra,
-    knitr,
     lifecycle,
     magrittr,
     methods,
@@ -96,11 +85,14 @@ Imports:
     stringi,
     stringr,
     testit,
-    testthat,
     tibble,
     tidyRSS,
     tidyselect,
     tools,
     utils,
     zen4R
 VignetteBuilder: knitr
+Suggests: 
+    knitr,
+    pkgload,
+    testthat
diff --git a/R/fn_make.R b/R/fn_make.R
@@ -50,10 +50,14 @@ make_additions_tb <- function (category_chr = character(0), library_chr = charac
 #' @importFrom kableExtra cell_spec kable kable_styling column_spec spec_image
 #' @examplesIf interactive()
 #'   # Likely to take more than one minute to execute.
-#'   make_code_releases_tbl("Framework", gh_repo_1L_chr = "ready4-dev/ready4")
-#'   make_code_releases_tbl("Module", gh_repo_1L_chr = "ready4-dev/ready4")
-#'   make_code_releases_tbl("Program", gh_repo_1L_chr = "ready4-dev/ready4")
-#'   make_code_releases_tbl("Subroutine", gh_repo_1L_chr = "ready4-dev/ready4")
+#'   make_code_releases_tbl("Framework",
+#'                          gh_repo_1L_chr = "ready4-dev/ready4")
+#'   make_code_releases_tbl("Module",
+#'                          gh_repo_1L_chr = "ready4-dev/ready4")
+#'   make_code_releases_tbl("Program",
+#'                          gh_repo_1L_chr = "ready4-dev/ready4")
+#'   make_code_releases_tbl("Subroutine",
+#'                          gh_repo_1L_chr = "ready4-dev/ready4")
 make_code_releases_tbl <- function (repo_type_1L_chr = c("Framework", "Module", "Package", 
     "Program", "Subroutine", "Program_and_Subroutine"), as_kbl_1L_lgl = T, 
     brochure_repos_chr = character(0), exclude_chr = character(0), 
@@ -780,8 +784,10 @@ make_modules_tb <- function (pkg_extensions_tb = NULL, cls_extensions_tb = NULL,
 #' @importFrom kableExtra cell_spec kable kable_styling
 #' @examplesIf interactive()
 #'   # Likely to take more than one minute to execute.
-#'   make_programs_tbl("Program", gh_repo_1L_chr = "ready4-dev/ready4")
-#'   make_programs_tbl("Subroutine", gh_repo_1L_chr = "ready4-dev/ready4")
+#'   make_programs_tbl("Program",
+#'                     gh_repo_1L_chr = "ready4-dev/ready4")
+#'   make_programs_tbl("Subroutine",
+#'                     gh_repo_1L_chr = "ready4-dev/ready4")
 make_programs_tbl <- function (what_1L_chr = c("Program", "Subroutine", "Program_and_Subroutine"), 
     as_kbl_1L_lgl = F, exclude_chr = character(0), format_1L_chr = "%d-%b-%Y", 
     gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_chr = "Documentation_0.0", 

diff --git a/R/fn_write.R b/R/fn_write.R
@@ -1316,7 +1316,8 @@ write_to_publish_dv_ds <- function (dv_ds_1L_chr, consent_1L_chr = "", consent_i
 #'   # Copy template RMD files
 #'   write_to_copy_rmds(dir_path_1L_chr = tempdir(),
 #'                      fl_nm_1L_chr = "RMDs",
-#'                      rmds_dir_1L_chr = system.file("MD_RMDs", package = "ready4"))
+#'                      rmds_dir_1L_chr = system.file("MD_RMDs",
+#'                                                    package = "ready4"))
 #'   # Typically you would now edit these templates before proceeding.
 #'   # Render post from RMD files.
 #'   write_to_render_post("RMDs", path_to_main_dir_1L_chr = tempdir())
@@ -1326,10 +1327,13 @@ write_to_publish_dv_ds <- function (dv_ds_1L_chr, consent_1L_chr = "", consent_i
 #'   # Copy template Rmarkdown file
 #'   write_to_copy_rmds(dir_path_1L_chr = tempdir(),
 #'                      fl_nm_1L_chr = "Rmarkdown",
-#'                      rmds_dir_1L_chr = system.file("MD_Rmarkdown", package = "ready4"))
+#'                      rmds_dir_1L_chr = system.file("MD_Rmarkdown",
+#'                                                    package = "ready4"))
 #'   # Typically you would now edit these templates before proceeding.
 #'   # Render post from RMD files.
-#'   write_to_render_post("Rmarkdown", path_to_main_dir_1L_chr = tempdir(), is_rmd_1L_lgl = F)
+#'   write_to_render_post("Rmarkdown",
+#'                        path_to_main_dir_1L_chr = tempdir(),
+#'                        is_rmd_1L_lgl = F)
 write_to_render_post <- function (included_dirs_chr, path_to_main_dir_1L_chr, consent_1L_chr = "", 
     consent_indcs_int = 1L, is_rmd_1L_lgl = T, options_chr = c("Y", 
         "N")) 

diff --git a/data-raw/DATASET.R b/data-raw/DATASET.R
@@ -107,7 +107,7 @@ c(readLines("R/imp_fns.R"), # update in ready4fun
   "NULL"
 ) %>%
   writeLines("R/imp_fns.R")
-write_examples()
+write_examples(consent_1L_chr = "Y")
 usethis::use_cran_badge() # Export to ready4fun
 devtools::build_vignettes()
 #

diff --git a/data-raw/examples/get_from_lup_obj.R b/data-raw/examples/get_from_lup_obj.R
@@ -1,4 +1,7 @@
-lookup_tb <- tibble::tibble(Name = c("Sajid","Siobhan"), Treat = c("Cake", "Chocolate"))
-get_from_lup_obj(lookup_tb, match_value_xx = "Siobhan", match_var_nm_1L_chr = "Name", target_var_nm_1L_chr = "Treat")
-get_from_lup_obj(lookup_tb, match_value_xx = "Cake", match_var_nm_1L_chr = "Treat", target_var_nm_1L_chr = "Name")
+lookup_tb <- tibble::tibble(Name = c("Sajid","Siobhan"),
+                            Treat = c("Cake", "Chocolate"))
+get_from_lup_obj(lookup_tb, match_value_xx = "Siobhan",
+                 match_var_nm_1L_chr = "Name", target_var_nm_1L_chr = "Treat")
+get_from_lup_obj(lookup_tb, match_value_xx = "Cake",
+                 match_var_nm_1L_chr = "Treat", target_var_nm_1L_chr = "Name")
 
diff --git a/data-raw/examples/make_code_releases_tbl.R b/data-raw/examples/make_code_releases_tbl.R
@@ -1,7 +1,11 @@
 if (interactive()) {
   # Likely to take more than one minute to execute.
-  make_code_releases_tbl("Framework", gh_repo_1L_chr = "ready4-dev/ready4")
-  make_code_releases_tbl("Module", gh_repo_1L_chr = "ready4-dev/ready4")
-  make_code_releases_tbl("Program", gh_repo_1L_chr = "ready4-dev/ready4")
-  make_code_releases_tbl("Subroutine", gh_repo_1L_chr = "ready4-dev/ready4")
+  make_code_releases_tbl("Framework",
+                         gh_repo_1L_chr = "ready4-dev/ready4")
+  make_code_releases_tbl("Module",
+                         gh_repo_1L_chr = "ready4-dev/ready4")
+  make_code_releases_tbl("Program",
+                         gh_repo_1L_chr = "ready4-dev/ready4")
+  make_code_releases_tbl("Subroutine",
+                         gh_repo_1L_chr = "ready4-dev/ready4")
   }
diff --git a/data-raw/examples/make_ds_releases_tbl.R b/data-raw/examples/make_ds_releases_tbl.R
@@ -1 +1 @@
-make_ds_releases_tbl("10.7910/DVN/RIQTKK", as_kbl_1L_lgl = F)
+make_ds_releases_tbl("10.7910/DVN/RIQTKK", as_kbl_1L_lgl = FALSE)
diff --git a/data-raw/examples/make_programs_tbl.R b/data-raw/examples/make_programs_tbl.R
@@ -1,5 +1,7 @@
 if (interactive()) {
   # Likely to take more than one minute to execute.
-  make_programs_tbl("Program", gh_repo_1L_chr = "ready4-dev/ready4")
-  make_programs_tbl("Subroutine", gh_repo_1L_chr = "ready4-dev/ready4")
+  make_programs_tbl("Program",
+                    gh_repo_1L_chr = "ready4-dev/ready4")
+  make_programs_tbl("Subroutine",
+                    gh_repo_1L_chr = "ready4-dev/ready4")
   }
diff --git a/data-raw/examples/print_data.R b/data-raw/examples/print_data.R
@@ -1,5 +1,5 @@
 datasets_tb <- get_datasets_tb("ready4-dev/ready4")
-print_data(datasets_tb, by_dv_1L_lgl = T)
+print_data(datasets_tb, by_dv_1L_lgl = TRUE)
 print_data(datasets_tb, what_1L_chr = "real")
 print_data(datasets_tb, what_1L_chr = "fakes")
 
diff --git a/data-raw/examples/print_packages.R b/data-raw/examples/print_packages.R
@@ -1,2 +1,4 @@
-print_packages(gh_repo_1L_chr = "ready4-dev/ready4", include_1L_chr = "framework")
-print_packages(gh_repo_1L_chr = "ready4-dev/ready4", include_1L_chr = "modules")
+print_packages(gh_repo_1L_chr = "ready4-dev/ready4",
+               include_1L_chr = "framework")
+print_packages(gh_repo_1L_chr = "ready4-dev/ready4",
+               include_1L_chr = "modules")
diff --git a/data-raw/examples/write_to_render_post.R b/data-raw/examples/write_to_render_post.R
@@ -5,7 +5,8 @@ if (interactive()) {
   # Copy template RMD files
   write_to_copy_rmds(dir_path_1L_chr = tempdir(),
                      fl_nm_1L_chr = "RMDs",
-                     rmds_dir_1L_chr = system.file("MD_RMDs", package = "ready4"))
+                     rmds_dir_1L_chr = system.file("MD_RMDs",
+                                                   package = "ready4"))
   # Typically you would now edit these templates before proceeding.
   # Render post from RMD files.
   write_to_render_post("RMDs", path_to_main_dir_1L_chr = tempdir())
@@ -15,8 +16,11 @@ if (interactive()) {
   # Copy template Rmarkdown file
   write_to_copy_rmds(dir_path_1L_chr = tempdir(),
                      fl_nm_1L_chr = "Rmarkdown",
-                     rmds_dir_1L_chr = system.file("MD_Rmarkdown", package = "ready4"))
+                     rmds_dir_1L_chr = system.file("MD_Rmarkdown",
+                                                   package = "ready4"))
   # Typically you would now edit these templates before proceeding.
   # Render post from RMD files.
-  write_to_render_post("Rmarkdown", path_to_main_dir_1L_chr = tempdir(), is_rmd_1L_lgl = F)
+  write_to_render_post("Rmarkdown",
+                       path_to_main_dir_1L_chr = tempdir(),
+                       is_rmd_1L_lgl = F)
   }
diff --git a/man/examples/get_from_lup_obj.R b/man/examples/get_from_lup_obj.R
@@ -1,4 +1,7 @@
-lookup_tb <- tibble::tibble(Name = c("Sajid","Siobhan"), Treat = c("Cake", "Chocolate"))
-get_from_lup_obj(lookup_tb, match_value_xx = "Siobhan", match_var_nm_1L_chr = "Name", target_var_nm_1L_chr = "Treat")
-get_from_lup_obj(lookup_tb, match_value_xx = "Cake", match_var_nm_1L_chr = "Treat", target_var_nm_1L_chr = "Name")
+lookup_tb <- tibble::tibble(Name = c("Sajid","Siobhan"),
+                            Treat = c("Cake", "Chocolate"))
+get_from_lup_obj(lookup_tb, match_value_xx = "Siobhan",
+                 match_var_nm_1L_chr = "Name", target_var_nm_1L_chr = "Treat")
+get_from_lup_obj(lookup_tb, match_value_xx = "Cake",
+                 match_var_nm_1L_chr = "Treat", target_var_nm_1L_chr = "Name")
 
diff --git a/man/examples/make_code_releases_tbl.R b/man/examples/make_code_releases_tbl.R
@@ -1,7 +1,11 @@
 if (interactive()) {
   # Likely to take more than one minute to execute.
-  make_code_releases_tbl("Framework", gh_repo_1L_chr = "ready4-dev/ready4")
-  make_code_releases_tbl("Module", gh_repo_1L_chr = "ready4-dev/ready4")
-  make_code_releases_tbl("Program", gh_repo_1L_chr = "ready4-dev/ready4")
-  make_code_releases_tbl("Subroutine", gh_repo_1L_chr = "ready4-dev/ready4")
+  make_code_releases_tbl("Framework",
+                         gh_repo_1L_chr = "ready4-dev/ready4")
+  make_code_releases_tbl("Module",
+                         gh_repo_1L_chr = "ready4-dev/ready4")
+  make_code_releases_tbl("Program",
+                         gh_repo_1L_chr = "ready4-dev/ready4")
+  make_code_releases_tbl("Subroutine",
+                         gh_repo_1L_chr = "ready4-dev/ready4")
   }
diff --git a/man/examples/make_ds_releases_tbl.R b/man/examples/make_ds_releases_tbl.R
@@ -1 +1 @@
-make_ds_releases_tbl("10.7910/DVN/RIQTKK", as_kbl_1L_lgl = F)
+make_ds_releases_tbl("10.7910/DVN/RIQTKK", as_kbl_1L_lgl = FALSE)
diff --git a/man/examples/make_programs_tbl.R b/man/examples/make_programs_tbl.R
@@ -1,5 +1,7 @@
 if (interactive()) {
   # Likely to take more than one minute to execute.
-  make_programs_tbl("Program", gh_repo_1L_chr = "ready4-dev/ready4")
-  make_programs_tbl("Subroutine", gh_repo_1L_chr = "ready4-dev/ready4")
+  make_programs_tbl("Program",
+                    gh_repo_1L_chr = "ready4-dev/ready4")
+  make_programs_tbl("Subroutine",
+                    gh_repo_1L_chr = "ready4-dev/ready4")
   }
diff --git a/man/examples/print_data.R b/man/examples/print_data.R
@@ -1,5 +1,5 @@
 datasets_tb <- get_datasets_tb("ready4-dev/ready4")
-print_data(datasets_tb, by_dv_1L_lgl = T)
+print_data(datasets_tb, by_dv_1L_lgl = TRUE)
 print_data(datasets_tb, what_1L_chr = "real")
 print_data(datasets_tb, what_1L_chr = "fakes")
 
diff --git a/man/examples/print_packages.R b/man/examples/print_packages.R
@@ -1,2 +1,4 @@
-print_packages(gh_repo_1L_chr = "ready4-dev/ready4", include_1L_chr = "framework")
-print_packages(gh_repo_1L_chr = "ready4-dev/ready4", include_1L_chr = "modules")
+print_packages(gh_repo_1L_chr = "ready4-dev/ready4",
+               include_1L_chr = "framework")
+print_packages(gh_repo_1L_chr = "ready4-dev/ready4",
+               include_1L_chr = "modules")
diff --git a/man/examples/write_to_render_post.R b/man/examples/write_to_render_post.R
@@ -5,7 +5,8 @@ if (interactive()) {
   # Copy template RMD files
   write_to_copy_rmds(dir_path_1L_chr = tempdir(),
                      fl_nm_1L_chr = "RMDs",
-                     rmds_dir_1L_chr = system.file("MD_RMDs", package = "ready4"))
+                     rmds_dir_1L_chr = system.file("MD_RMDs",
+                                                   package = "ready4"))
   # Typically you would now edit these templates before proceeding.
   # Render post from RMD files.
   write_to_render_post("RMDs", path_to_main_dir_1L_chr = tempdir())
@@ -15,8 +16,11 @@ if (interactive()) {
   # Copy template Rmarkdown file
   write_to_copy_rmds(dir_path_1L_chr = tempdir(),
                      fl_nm_1L_chr = "Rmarkdown",
-                     rmds_dir_1L_chr = system.file("MD_Rmarkdown", package = "ready4"))
+                     rmds_dir_1L_chr = system.file("MD_Rmarkdown",
+                                                   package = "ready4"))
   # Typically you would now edit these templates before proceeding.
   # Render post from RMD files.
-  write_to_render_post("Rmarkdown", path_to_main_dir_1L_chr = tempdir(), is_rmd_1L_lgl = F)
+  write_to_render_post("Rmarkdown",
+                       path_to_main_dir_1L_chr = tempdir(),
+                       is_rmd_1L_lgl = F)
   }
diff --git a/man/get_from_lup_obj.Rd b/man/get_from_lup_obj.Rd
diff --git a/man/make_code_releases_tbl.Rd b/man/make_code_releases_tbl.Rd
diff --git a/man/make_ds_releases_tbl.Rd b/man/make_ds_releases_tbl.Rd
diff --git a/man/make_programs_tbl.Rd b/man/make_programs_tbl.Rd
diff --git a/man/print_data.Rd b/man/print_data.Rd
diff --git a/man/print_packages.Rd b/man/print_packages.Rd
diff --git a/man/write_to_render_post.Rd b/man/write_to_render_post.Rd