documentation website function update and vignete update

Author: matthewphamilton

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 0.0.1. Zenodo. https://doi.org/10.5281/zenodo.5606250"
+message: "Matthew P Hamilton  (2024). ready4: Develop and Use Modular Health Economic Models. Version 0.1.20. 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: 0.0.1
+version: 0.1.20
 doi: 10.5281/zenodo.5606250
-date-released: 2025-12-10
+date-released: 2026-01-29
 url: "https://ready4-dev.github.io/ready4/"

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
@@ -30,8 +30,6 @@ Collate:
     'C4_Ready4Private.R'
     'C4_Ready4Project.R'
     'C4_Ready4Public.R'
-    'add.R'
-    'bind.R'
     'fn_add.R'
     'fn_bind.R'
     'fn_get.R'
@@ -42,11 +40,9 @@ 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'
@@ -63,34 +59,31 @@ 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,
@@ -99,6 +92,5 @@ Imports:
     tidyRSS,
     tidyselect,
     tools,
-    usethis,
-    utils,
-    zen4R
+    utils
+Language: en-AU

R/fn_get.R

@@ -248,7 +248,7 @@ get_excluded_repos <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_
         dmt_urls_chr <- dmt_urls_xx
         if (any(dmt_urls_chr %>% endsWith("exclude_chr.RDS"))) {
             exclude_chr <- get_gracefully(dmt_urls_chr[dmt_urls_chr %>% 
-                endsWith("exclude_chr.RDS")], not_chr_1L_lgl = TRUE)
+                endsWith("exclude_chr.RDS")], not_chr_1L_lgl = FALSE)
         }
         else {
             exclude_chr <- character(0)

R/fn_make.R

@@ -911,6 +911,7 @@ make_modules_tb <- function (pkg_extensions_tb = NULL, cls_extensions_tb = NULL,
 #' @param format_1L_chr Format (a character vector of length one), Default: '%d-%b-%Y'
 #' @param gh_repo_1L_chr Github repository (a character vector of length one), Default: 'ready4-dev/ready4'
 #' @param gh_tag_1L_chr Github tag (a character vector of length one), Default: 'Documentation_0.0'
+#' @param org_1L_chr Organisation (a character vector of length one), Default: 'ready4-dev'
 #' @param tidy_desc_1L_lgl Tidy description (a logical vector of length one), Default: TRUE
 #' @param url_stub_1L_chr Url stub (a character vector of length one), Default: 'https://ready4-dev.github.io/'
 #' @param zenodo_1L_chr Zenodo (a character vector of length one), Default: 'ready4'
@@ -935,7 +936,7 @@ make_modules_tb <- function (pkg_extensions_tb = NULL, cls_extensions_tb = NULL,
 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", 
-    tidy_desc_1L_lgl = TRUE, url_stub_1L_chr = "https://ready4-dev.github.io/", 
+    org_1L_chr = "ready4-dev", tidy_desc_1L_lgl = TRUE, url_stub_1L_chr = "https://ready4-dev.github.io/", 
     zenodo_1L_chr = "ready4", ...) 
 {
     if (!requireNamespace("zen4R", quietly = TRUE)) {
@@ -944,8 +945,8 @@ make_programs_tbl <- function (what_1L_chr = c("Program", "Subroutine", "Program
     what_1L_chr <- match.arg(what_1L_chr)
     programs_xx <- make_code_releases_tbl(what_1L_chr, as_kbl_1L_lgl = FALSE, 
         exclude_chr = exclude_chr, gh_repo_1L_chr = gh_repo_1L_chr, 
-        gh_tag_1L_chr = gh_tag_1L_chr, tidy_desc_1L_lgl = FALSE, 
-        url_stub_1L_chr = url_stub_1L_chr)
+        gh_tag_1L_chr = gh_tag_1L_chr, org_1L_chr = org_1L_chr, 
+        tidy_desc_1L_lgl = FALSE, url_stub_1L_chr = url_stub_1L_chr)
     if (!is.null(programs_xx)) {
         programs_xx <- programs_xx %>% dplyr::group_by(!!rlang::sym(what_1L_chr)) %>% 
             dplyr::filter(dplyr::row_number() == 1) %>% dplyr::arrange(!!rlang::sym(what_1L_chr)) %>% 

data-raw/NOTES.R

@@ -22,9 +22,16 @@ module_libraries_ls <- list(People = list(names_chr = c("youthvars", "scorz", "s
                                           descriptions_chr = c("Description (datasets)", "Description (variable scoring)", "Modelling (inverse problems)", "Modelling (health utility)", "Prediction (health utility)", "Modelling (choice)", "Modelling (heterogeneity)")),
                             Places = list(names_chr = c("aus", "vicinity"),
                                           descriptions_chr = c("Modelling (Australian spatial)", "Modelling (spatial)")),
-                            #Platforms = ,
-                            Programs = list(names_chr = c("bimp", "costly"),
-                                            descriptions_chr = c("Modelling (budget impact)", "Modelling (costs)")))
+                            Platforms = list(names_chr = c("mimic"),
+                                             descriptions_chr = c("Modelling (microsimulation)")),
+                            Programs = list(names_chr = c(
+                              # "bimp",
+                                                          "costly",
+                                                          "serious"),
+                                            descriptions_chr = c(
+                                              # "Modelling (budget impact)",
+                                                                 "Modelling (costs)",
+                                                                 "Modelling (time series)")))
 extras_tb <- module_libraries_ls  %>% # c("people", "places","platforms","programs")
   purrr::map2_dfr(names(module_libraries_ls),
                   ~make_additions_tb(library_chr = .x$names_chr,#make_modules_pkgs_chr(.x),
@@ -63,11 +70,11 @@ Y <- renewSlot(Y,
                  #classes_bup_lup =  Y@b_Ready4useIngest@objects_ls$bup_classes_lup
                  #classes_lup = Z@b_Ready4useIngest@objects_ls$framework_metadata_ls$classes_lup
                  #abbreviations_lup = abbreviations_lup,
-                 #libraries_tb = libraries_tb
+                 libraries_tb = libraries_tb,
                  #exclude_chr = c("aus_09_synth","dce_sa_cards","fakefolk","rebuild")
-                 #libraries_ls = libraries_ls
-                 methods_tb = methods_tb
-                 #modules_tb = modules_tb
+                 libraries_ls = libraries_ls,
+                 # methods_tb = methods_tb
+                 modules_tb = modules_tb
                  #treat_as_words_chr = Y@b_Ready4useIngest@objects_ls$treat_as_words_chr
                  )),
                slot_nm_1L_chr = "b_Ready4useIngest")

data-raw/fns/get.R

@@ -153,19 +153,19 @@ get_examples <- function(vignettes_chr,
   }
   return(examples_chr)
 }
-get_excluded_repos <- function(gh_repo_1L_chr = "ready4-dev/ready4",
-                                 gh_tag_1L_chr = "Documentation_0.0"){
+get_excluded_repos <- function (gh_repo_1L_chr = "ready4-dev/ready4", gh_tag_1L_chr = "Documentation_0.0"){
   exclude_chr <- NULL
   dmt_urls_xx <- get_gracefully(NULL, fn = piggyback::pb_download_url,
-                                args_ls = list(repo = gh_repo_1L_chr, tag = gh_tag_1L_chr, .token = ""),
-                                not_chr_1L_lgl = FALSE)
-  if(!is.null(dmt_urls_xx)){
-  dmt_urls_chr <- dmt_urls_xx
-  if(any(dmt_urls_chr %>% endsWith("exclude_chr.RDS"))){
-    exclude_chr <- get_gracefully(dmt_urls_chr[dmt_urls_chr %>% endsWith("exclude_chr.RDS")], not_chr_1L_lgl = TRUE)
-  }else{
-    exclude_chr <- character(0)
-  }
+                                args_ls = list(repo = gh_repo_1L_chr, tag = gh_tag_1L_chr,
+                                               .token = ""), not_chr_1L_lgl = FALSE)
+  if (!is.null(dmt_urls_xx)) {
+    dmt_urls_chr <- dmt_urls_xx
+    if (any(dmt_urls_chr %>% endsWith("exclude_chr.RDS"))) {
+      exclude_chr <- get_gracefully(dmt_urls_chr[dmt_urls_chr %>%
+                                                   endsWith("exclude_chr.RDS")], not_chr_1L_lgl = FALSE)
+    } else {
+      exclude_chr <- character(0)
+    }
   }
   return(exclude_chr)
 }