redo of examples

ready4-dev · Jul 4, 2024 · 5e61b11 · 5e61b11
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diff --git a/CITATION.cff b/CITATION.cff
@@ -1,10 +1,10 @@
 cff-version: 1.2.0
-message: "Matthew P Hamilton  (2024). ready4: Develop and Use Modular Health Economic Models. Version 0.1.12. Zenodo. https://doi.org/10.5281/zenodo.5606250"
+message: "Matthew P Hamilton  (2024). ready4: Develop and Use Modular Health Economic Models. Version 0.1.13. Zenodo. https://doi.org/10.5281/zenodo.5606250"
 authors:
   - family-names: "Hamilton"
     given-names: "Matthew P"
 title: "ready4: Develop and Use Modular Health Economic Models"
-version: 0.1.12
+version: 0.1.13
 doi: 10.5281/zenodo.5606250
-date-released: 2024-07-04
+date-released: 2024-07-05
 url: "https://ready4-dev.github.io/ready4/"
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.1.9
-Date: 2024-04-15 11:10:46 UTC
-SHA: 3fb2975f30abb3a753d7d22f7781862c91b4e287
+Version: 0.1.12
+Date: 2024-07-04 19:38:43 UTC
+SHA: 3b7cc823fa3a88283d57502358e888e0a7688d2c
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -19,7 +19,7 @@ Description: A template model module, tools to help find model modules
     use it visit <https://www.ready4-dev.com/>. For a background to the
     methodological issues that the framework is attempting to help solve,
     see Hamilton et al. (2024) <doi:10.1007/s40273-024-01378-8>.
-License: GPL-3 + file LICENSE
+License: GPL-3
 URL: https://ready4-dev.github.io/ready4/,
     https://github.com/ready4-dev/ready4, https://www.ready4-dev.com/
 Encoding: UTF-8
@@ -29,8 +29,6 @@ Collate:
     'C4_Ready4Module.R'
     'C4_Ready4Private.R'
     'C4_Ready4Public.R'
-    'add.R'
-    'bind.R'
     'fn_add.R'
     'fn_bind.R'
     'fn_get.R'
@@ -41,11 +39,9 @@ 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'
@@ -62,34 +58,31 @@ 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'
 Suggests: 
+    devtools,
+    Hmisc,
     knitr,
-    testthat
+    pkgload,
+    readr,
+    readxl,
+    rmarkdown,
+    testthat,
+    usethis,
+    zen4R
 VignetteBuilder: knitr
 Imports: 
     curl,
     dataverse,
-    devtools,
     dplyr,
     gh,
-    Hmisc,
     kableExtra,
     lifecycle,
     magrittr,
     methods,
     piggyback,
     purrr,
-    readr,
-    readxl,
     rlang,
-    rmarkdown,
     rvest,
     stats,
     stringi,
@@ -98,6 +91,4 @@ Imports:
     tidyRSS,
     tidyselect,
     tools,
-    usethis,
-    utils,
-    zen4R
+    utils
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,5 @@
 # ready4 0.1.13
+This patch updates one of the examples files so that its execution does not breach the CRAN recommended run time limit.
 
 # ready4 0.1.12
 This patch updates functions for printing HTML tables to return NULL values if supplied with NULL values instead of tibble objects.

diff --git a/R/fn_get.R b/R/fn_get.R
@@ -126,6 +126,7 @@ get_cls_extensions <- function (pkg_extensions_tb, gh_repo_1L_chr = "ready4-dev/
 #' @importFrom piggyback pb_download_url
 #' @keywords internal
 #' @example man/examples/get_datasets_tb.R
+#' @example man/examples/get_datasets_tb.R
 get_datasets_tb <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_chr = "Documentation_0.0", 
     rds_fl_name_1L_chr = "datasets_tb") 
 {
@@ -323,6 +324,7 @@ get_fl_nm_from_path <- function (path_1L_chr)
 #' @importFrom rlang sym
 #' @importFrom stringr str_detect str_locate str_sub
 #' @example man/examples/get_from_lup_obj.R
+#' @example man/examples/get_from_lup_obj.R
 get_from_lup_obj <- function (data_lookup_tb, match_value_xx, match_var_nm_1L_chr, 
     target_var_nm_1L_chr, evaluate_1L_lgl = FALSE) 
 {
@@ -478,6 +480,44 @@ get_gh_repos <- function (org_1L_chr)
 #' @importFrom purrr map_lgl
 #' @importFrom stringr str_detect
 #' @example man/examples/get_gracefully.R
+#' @examplesIf interactive()
+#'   # Likely to take more than one minute to execute.
+#' get_gracefully(paste0("https://github.com/ready4-dev/ready4/",
+#'                       "releases/download/Documentation_0.0/ready4_badges_lup.RDS"))
+#'   get_gracefully("DOES NOT EXIST")
+#' if(requireNamespace("dataverse", quietly = TRUE)) {
+#'   get_gracefully("https://doi.org/10.7910/DVN/RIQTKK", fn = dataverse::dataset_files,
+#'                  args_ls = list(key = NULL, server = "dataverse.harvard.edu"))
+#'     get_gracefully("https://doi.org/10.7910/DVN/RIQTKK", fn = dataverse::dataset_files,
+#'                    args_ls = list(key = NULL, server = "DOES_NOT_EXIST"))
+#'     get_gracefully("DOES_NOT_EXIST", fn = dataverse::dataset_files,
+#'                    args_ls = list(key = NULL, server = "dataverse.harvard.edu"))
+#' 
+#' }
+#' if (requireNamespace("gh", quietly = TRUE)) {
+#'   get_gracefully("/orgs/ready4-dev/repos", fn = gh::gh, args_ls=list(type = "public"))
+#'       get_gracefully("DOES_NOT_EXIST", fn = gh::gh, args_ls=list(type = "public"))
+#' }
+#' if(requireNamespace("piggyback", quietly = TRUE)) {
+#'   get_gracefully(NULL, fn = piggyback::pb_download_url,
+#'                  args_ls = list(repo = "ready4-dev/ready4",
+#'                                 tag = "Documentation_0.0",
+#'                                 .token = ""))
+#'     get_gracefully(NULL, fn = piggyback::pb_download_url,
+#'                    args_ls = list(repo = "DOES_NOT_EXIST",
+#'                                   tag = "DOES_NOT_EXIST",
+#'                                   .token = ""))
+#' }
+#' if(requireNamespace("rvest", quietly = TRUE)) {
+#'   get_gracefully("https://ready4-dev.github.io/ready4/index.html", fn=rvest::read_html)
+#'     get_gracefully("DOES_NOT_EXIST", fn=rvest::read_html)
+#' }
+#' 
+#' if(requireNamespace("tidyRSS", quietly = TRUE)) {
+#'   get_gracefully("https://github.com/ready4-dev/ready4/releases.atom",
+#'                  fn = tidyRSS::tidyfeed)
+#'     get_gracefully("DOES_NOT_EXIST", fn = tidyRSS::tidyfeed)
+#' }
 get_gracefully <- function (url_1L_chr, args_ls = NULL, fn = readRDS, not_chr_1L_lgl = F, 
     tests_chr = character(0)) 
 {
@@ -556,6 +596,7 @@ get_libraries_ls <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_ch
 #' @export 
 #' @importFrom piggyback pb_download_url
 #' @example man/examples/get_libraries_tb.R
+#' @example man/examples/get_libraries_tb.R
 get_libraries_tb <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_chr = "Documentation_0.0") 
 {
     libraries_tb <- NULL
@@ -606,6 +647,7 @@ get_manual_urls <- function (pkg_nm_1L_chr = "ready4", pkg_url_1L_chr = "https:/
 #' @export 
 #' @importFrom stringr str_detect str_remove_all
 #' @example man/examples/get_methods.R
+#' @example man/examples/get_methods.R
 get_methods <- function (pkg_nm_1L_chr = "ready4", cls_nm_1L_chr = "Ready4Module") 
 {
     methods_chr <- showMethods(classes = "Ready4Module", printTo = FALSE)
@@ -626,6 +668,7 @@ get_methods <- function (pkg_nm_1L_chr = "ready4", cls_nm_1L_chr = "Ready4Module
 #' @export 
 #' @importFrom piggyback pb_download_url
 #' @example man/examples/get_methods_tb.R
+#' @example man/examples/get_methods_tb.R
 get_methods_tb <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_chr = "Documentation_0.0") 
 {
     methods_tb <- NULL
@@ -648,6 +691,7 @@ get_methods_tb <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_chr
 #' @export 
 #' @importFrom piggyback pb_download_url
 #' @example man/examples/get_modules_tb.R
+#' @example man/examples/get_modules_tb.R
 get_modules_tb <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_chr = "Documentation_0.0") 
 {
     modules_tb <- NULL

diff --git a/R/fn_make.R b/R/fn_make.R
@@ -59,6 +59,18 @@ make_additions_tb <- function (category_chr = character(0), library_chr = charac
 #'       make_code_releases_tbl("Subroutine",
 #'                              gh_repo_1L_chr = "ready4-dev/ready4")
 #'     }
+#' @examplesIf interactive()
+#'   # Likely to take more than one minute to execute.
+#'     if(requireNamespace("tidyRSS", quietly = TRUE)) {
+#'       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 = TRUE, 
     brochure_repos_chr = character(0), exclude_chr = character(0), 
@@ -196,6 +208,16 @@ make_code_releases_tbl <- function (repo_type_1L_chr = c("Framework", "Module",
 #'   make_datasets_tb("ready4", dvs_tb = dvs_tb, type_1L_chr = "datasets")
 #'   make_datasets_tb("ready4", dvs_tb = dvs_tb, type_1L_chr = "datasets", what_1L_chr = "real")
 #'   make_datasets_tb("ready4", dvs_tb = dvs_tb, type_1L_chr = "datasets", what_1L_chr = "fakes")
+#' @examplesIf interactive()
+#'   # Likely to take more than one minute to execute.
+#'   make_datasets_tb("ready4")
+#'   dvs_tb <- get_datasets_tb("ready4-dev/ready4")
+#'   make_datasets_tb("ready4", dvs_tb = dvs_tb)
+#'   make_datasets_tb("ready4", dvs_tb = dvs_tb, what_1L_chr = "real")
+#'   make_datasets_tb("ready4", dvs_tb = dvs_tb, what_1L_chr = "fakes")
+#'   make_datasets_tb("ready4", dvs_tb = dvs_tb, type_1L_chr = "datasets")
+#'   make_datasets_tb("ready4", dvs_tb = dvs_tb, type_1L_chr = "datasets", what_1L_chr = "real")
+#'   make_datasets_tb("ready4", dvs_tb = dvs_tb, type_1L_chr = "datasets", what_1L_chr = "fakes")
 make_datasets_tb <- function (dv_nm_1L_chr = "ready4", dvs_tb = NULL, filter_cdns_ls = NULL, 
     key_1L_chr = NULL, server_1L_chr = "dataverse.harvard.edu", 
     toy_data_dv_1L_chr = "fakes", type_1L_chr = c("collections", 
@@ -312,6 +334,7 @@ make_datasets_tb <- function (dv_nm_1L_chr = "ready4", dvs_tb = NULL, filter_cdn
 #' @importFrom dplyr arrange desc mutate filter select
 #' @importFrom kableExtra cell_spec kable kable_styling
 #' @example man/examples/make_ds_releases_tbl.R
+#' @example man/examples/make_ds_releases_tbl.R
 make_ds_releases_tbl <- function (ds_dois_chr, format_1L_chr = "%d-%b-%Y", key_1L_chr = NULL, 
     server_1L_chr = "dataverse.harvard.edu", as_kbl_1L_lgl = TRUE, 
     ...) 
@@ -696,6 +719,9 @@ make_local_path_to_dv_data <- function (save_dir_path_1L_chr, fl_nm_1L_chr, save
 #' @examplesIf interactive()
 #'   # Likely to take more than one minute to execute.
 #'   make_methods_tb(gh_repo_1L_chr = "ready4-dev/ready4")
+#' @examplesIf interactive()
+#'   # Likely to take more than one minute to execute.
+#'   make_methods_tb(gh_repo_1L_chr = "ready4-dev/ready4")
 make_methods_tb <- function (packages_tb = NULL, exclude_mthds_for_chr = NA_character_, 
     framework_only_1L_lgl = TRUE, gh_repo_1L_chr = "ready4-dev/ready4", 
     gh_tag_1L_chr = "Documentation_0.0", module_pkgs_chr = character(0), 
@@ -771,6 +797,9 @@ make_modules_pkgs_chr <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_
 #' @examplesIf interactive()
 #'   # Likely to take more than one minute to execute.
 #'   make_modules_tb(gh_repo_1L_chr = "ready4-dev/ready4")
+#' @examplesIf interactive()
+#'   # Likely to take more than one minute to execute.
+#'   make_modules_tb(gh_repo_1L_chr = "ready4-dev/ready4")
 make_modules_tb <- function (pkg_extensions_tb = NULL, cls_extensions_tb = NULL, 
     gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_chr = "Documentation_0.0", 
     module_pkgs_chr = character(0), include_1L_chr = "modules", 
@@ -917,6 +946,14 @@ make_modules_tb <- function (pkg_extensions_tb = NULL, cls_extensions_tb = NULL,
 #'     make_programs_tbl("Subroutine",
 #'                       gh_repo_1L_chr = "ready4-dev/ready4")
 #'   }
+#' @examplesIf interactive()
+#'   # Likely to take more than one minute to execute.
+#'   if(requireNamespace("zen4R", quietly = TRUE)) {
+#'     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 = FALSE, 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_print.R b/R/fn_print.R
@@ -13,6 +13,7 @@
 #' @rdname print_data
 #' @export 
 #' @example man/examples/print_data.R
+#' @example man/examples/print_data.R
 print_data <- function (datasets_tb, by_dv_1L_lgl = FALSE, filter_cdns_ls = NULL, 
     root_1L_chr = "https://dataverse.harvard.edu/dataverse/", 
     scroll_height_1L_chr = character(0), scroll_width_1L_chr = character(0), 
@@ -143,6 +144,7 @@ print_dvs <- function (dvs_tb, filter_cdns_ls = NULL, root_1L_chr = "https://dat
 #' @importFrom purrr map_chr
 #' @importFrom kableExtra kable kable_styling column_spec
 #' @example man/examples/print_methods.R
+#' @example man/examples/print_methods.R
 print_methods <- function (methods_tb = NULL, exclude_mthds_for_chr = NA_character_, 
     gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_chr = "Documentation_0.0", 
     methods_chr = NULL, module_pkgs_chr = character(0), ns_var_nm_1L_chr = "pt_ns_chr", 
@@ -189,6 +191,7 @@ print_methods <- function (methods_tb = NULL, exclude_mthds_for_chr = NA_charact
 #' @importFrom dplyr filter select
 #' @importFrom kableExtra kable kable_styling
 #' @example man/examples/print_modules.R
+#' @example man/examples/print_modules.R
 print_modules <- function (modules_tb, scroll_height_1L_chr = character(0), scroll_width_1L_chr = character(0), 
     what_1L_chr = "All", ...) 
 {
@@ -255,6 +258,26 @@ print_modules <- function (modules_tb, scroll_height_1L_chr = character(0), scro
 #'   ## Print module libraries
 #'   print_packages(gh_repo_1L_chr = "ready4-dev/ready4",
 #'                  include_1L_chr = "modules")
+#' @examplesIf interactive()
+#'   # Method 1
+#'   libraries_tb <- get_libraries_tb(gh_repo_1L_chr = "ready4-dev/ready4")
+#'   ## Print framework libraries
+#'   update_libraries_tb(libraries_tb,
+#'                       url_stub_1L_chr = "https://ready4-dev.github.io/",
+#'                       include_1L_chr = "framework") %>%
+#'     print_packages()
+#'   ## Print module libraries
+#'   update_libraries_tb(libraries_tb,
+#'                       url_stub_1L_chr = "https://ready4-dev.github.io/",
+#'                       include_1L_chr = "modules") %>%
+#'     print_packages()
+#'   # Method 2
+#'   ## Print framework libraries
+#'   print_packages(gh_repo_1L_chr = "ready4-dev/ready4",
+#'                  include_1L_chr = "framework")
+#'   ## Print module libraries
+#'   print_packages(gh_repo_1L_chr = "ready4-dev/ready4",
+#'                  include_1L_chr = "modules")
 print_packages <- function (pkg_extensions_tb = NULL, gh_repo_1L_chr = "ready4-dev/ready4", 
     gh_tag_1L_chr = "Documentation_0.0", include_1L_chr = "modules", 
     module_pkgs_chr = character(0), ns_var_nm_1L_chr = "pt_ns_chr",