updated dpcys

DESCRIPTION

@@ -17,16 +17,17 @@ Description: Tools for mapping measures routinely collected in youth
  youthu package has been made available as part of the process of
  testing and documenting the package. If you have any questions, please
  contact the authors ([email protected]).
-License: GPL-3 + file LICENSE
+License: GPL-3
 URL: https://ready4-dev.github.io/youthu/,
  https://github.com/ready4-dev/youthu, https://www.ready4-dev.com/
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Suggests: 
  knitr,
+ pkgload,
  rmarkdown,
- scorz,
+ scorz (>= 0.0.0.9065),
  testthat
 VignetteBuilder: knitr
 Imports: 
@@ -57,7 +58,8 @@ Imports:
 Depends: 
  R (>= 2.10)
 LazyData: true
-Remotes: 
+Remotes:  
  ready4-dev/ready4use,
  ready4-dev/specific,
- ready4-dev/youthvars
+ ready4-dev/youthvars,
+ ready4-dev/scorz

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export(":=")
+export(.data)
 export(add_change_in_ds_var)
 export(add_costs_by_tmpt)
 export(add_costs_from_gamma_dstr)
@@ -97,6 +99,8 @@ importFrom(ready4,get_from_lup_obj)
 importFrom(ready4,ingest)
 importFrom(ready4use,Ready4useRepos)
 importFrom(ready4use,add_labels_from_dictionary)
+importFrom(rlang,":=")
+importFrom(rlang,.data)
 importFrom(rlang,exec)
 importFrom(rlang,sym)
 importFrom(specific,add_utl_predn_to_new_ds)

R/imp_fns.R

@@ -1,23 +1,51 @@
 #' Pipe operator
 #'
-#' Implements: https://github.com/sckott/analogsea/issues/32
-#' and https://github.com/rstudio/ggvis/blob/master/R/pipe.R.
+#' Import of [magrittr::%>%()]. See magrittr package documentation for detailed description.
 #'
 #' @importFrom magrittr %>%
 #' @name %>%
 #' @rdname pipe
 #' @export
-#' @param lhs,rhs An object and a function to apply to it
 #' @keywords internal
+#' @returns The type of return from this function depends on the left hand side and right hand side arguments supplied to it. In principle, any type of returned object is feasible.
+#' @seealso [magrittr::%>%()]
 NULL
 
 #' Deprecated function
 #'
-#' Import of deprecated function as recommended in lifecycle package documentation.
+#' Import of [lifecycle::deprecated()]. See lifecycle package documentation for detailed description.
 #'
 #' @importFrom lifecycle deprecated
 #' @name deprecated
 #' @rdname deprecated
 #' @export
 #' @keywords internal
+#' @returns Does not return a value as the function is used to signal that a function argument has been deprecated.
+#' @seealso [lifecycle::deprecated()]
+NULL
+
+#' Non standard evaluation assignment function
+#'
+#' Import of := function, implementing [rlang::dyn-dots()]. See rlang package documentation for detailed description.
+#'
+#' @importFrom rlang :=
+#' @name :=
+#' @rdname nseequals
+#' @export
+#' @keywords internal
+#' @returns Does not return a value. Used to implement non standard evaluation within a dynamic dots context.
+#' @seealso [rlang::dyn-dots()]
+NULL
+
+#' Dot Data function
+#'
+#' Import of [rlang::.data()]. See rlang package documentation for detailed description.
+#'
+#' @importFrom rlang .data
+#' @name .data
+#' @rdname dotdata
+#' @export
+#' @keywords internal
+#' @returns Does not return a value. A pronoun for use in data-masked functions.
+#' @seealso [rlang::.data()]
 NULL

README.md

@@ -12,9 +12,9 @@
 
 Tools for mapping measures routinely collected in youth
 mental health services to Quality Adjusted Life Years (QALYs). Part of
-the ready4 youth mental health systems model
-(https://www.ready4-dev.com/docs/model/). This development version of
-the youthu package has been made available as part of the process of
+the ready4forwhatsnext youth mental health systems model
+(https://readyforwhatsnext.org/). This development version of the
+youthu package has been made available as part of the process of
 testing and documenting the package. If you have any questions, please
 contact the authors ([email protected]).
 

_pkgdown.yml

@@ -10,7 +10,7 @@ home:
  href: https://github.com/ready4-dev/youthu/releases/download/Documentation_0.0/youthu_User.pdf
  - text: Manual - Developer (PDF)
  href: https://github.com/ready4-dev/youthu/releases/download/Documentation_0.0/youthu_Developer.pdf
- - text: Framework and Model
+ - text: Model
  href: https://www.ready4-dev.com/
 development:
  mode: auto

data-raw/DATASET.R

@@ -2,6 +2,7 @@
 library(ready4)
 library(ready4show)
 library(ready4use)
+library(ready4fun)
 library(youthvars)
 library(scorz)
 library(specific)
@@ -10,9 +11,9 @@ ready4fun::write_fn_type_dirs()
 fns_env_ls <- ready4fun::read_fns(c("data-raw/fns/","data-raw/mthds/"),
  fns_env = new.env(parent = globalenv()))
 x <- ready4fun::make_pkg_desc_ls(pkg_title_1L_chr = "Transform Youth Outcomes to Health Utility Predictions" %>% tools::toTitleCase(),
- pkg_desc_1L_chr = "Tools for mapping measures routinely collected in youth mental health services to Quality Adjusted Life Years (QALYs). Part of the ready4 youth mental health systems model (https://www.ready4-dev.com/docs/model/).
+ pkg_desc_1L_chr = "Tools for mapping measures routinely collected in youth mental health services to Quality Adjusted Life Years (QALYs). Part of the ready4forwhatsnext youth mental health systems model (https://readyforwhatsnext.org/).
  This development version of the youthu package has been made available as part of the process of testing and documenting the package. If you have any questions, please contact the authors ([email protected]).",
- authors_prsn = c(utils::person(given = "Matthew",family = "Hamilton",email = "[email protected]", role = c("aut", "cre"),comment = c(ORCID = "0000-0001-7407-9194")),
+ authors_prsn = c(utils::person(given = "Matthew",family = "Hamilton",email = "[email protected]", role = c("aut", "cre", "cph"),comment = c(ORCID = "0000-0001-7407-9194")),
  utils::person(given = "Caroline",family = "Gao",email = "[email protected]", role = c("aut"),comment = c(ORCID = "0000-0002-0987-2759")),
  utils::person("Orygen", role = c("cph", "fnd")),
  utils::person("Headspace", role = c( "fnd")),
@@ -24,7 +25,7 @@ x <- ready4fun::make_pkg_desc_ls(pkg_title_1L_chr = "Transform Youth Outcomes to
  suggests_chr = c("knitr","rmarkdown", "scorz")),
  build_ignore_ls = ready4fun::make_build_ignore_ls(file_nms_chr = c("initial_setup.R")),
  check_type_1L_chr = "ready4",
- copyright_holders_chr = "Orygen",
+ copyright_holders_chr = "Matthew Hamilton and Orygen",
  custom_dmt_ls = ready4fun::make_custom_dmt_ls(user_manual_fns_chr = c("add_utl_predn",
  "add_qalys_to_ds",
  "get_mdl_from_dv",
@@ -34,7 +35,7 @@ x <- ready4fun::make_pkg_desc_ls(pkg_title_1L_chr = "Transform Youth Outcomes to
  "make_sngl_grp_ds",
  "make_matched_ds",
  "rename_from_nmd_vec")),##
- dev_pkgs_chr = c("ready4",
+ dev_pkgs_chr = c(#"ready4",
  "ready4use","ready4show",
  "scorz", "specific",
  "youthvars"),
@@ -58,12 +59,10 @@ z <- ready4::author(z)
 usethis::use_dev_package("scorz", type = "Suggests", remote = "ready4-dev/scorz")
 ready4::write_extra_pkgs_to_actions(path_to_dir_1L_chr = ".github/workflows", consent_1L_chr = "Y")
 write_to_edit_workflow("pkgdown.yaml", consent_1L_chr = "Y") # In other packages, run for "test-coverage.yaml" as well.
-readLines("_pkgdown.yml") %>%
- stringr::str_replace_all(" - text: Model", " - text: Framework & Model") %>%
- writeLines(con = "_pkgdown.yml")
-devtools::build_vignettes()
-# ready4::write_citation_cff(packageDescription("youthu"),
-# citation_chr = readLines("inst/CITATION"))
+write_to_tidy_pkg(z$x_ready4fun_manifest, build_vignettes_1L_lgl = TRUE,
+ clean_license_1L_lgl = TRUE, consent_1L_chr = "Y",
+ examples_chr = character(0),
+ suggest_chr = "pkgload")
 # usethis::use_dev_package("TTU",
 # type = "Depends",
 # remote = "ready4-dev/TTU")

inst/CITATION

@@ -4,11 +4,11 @@ bibentry(
  bibtype = "Manual",
  doi = "10.5281/zenodo.5646668",
  title = paste0(meta$Package,": ",meta$Title),
- author = c(person("Matthew Hamilton <[email protected]> [aut, cre]", "(<https://orcid.org/0000-0001-7407-9194>)"), person("Caroline Gao <[email protected]> [aut]", "(<https://orcid.org/0000-0002-0987-2759>)")),
+ author = c(person("Matthew Hamilton <[email protected]> [aut, cre, cph]", "(<https://orcid.org/0000-0001-7407-9194>)"), person("Caroline Gao <[email protected]> [aut]", "(<https://orcid.org/0000-0002-0987-2759>)")),
  year = "2024",
  note = sprintf("R package version %s", meta$Version),
  url = "https://ready4-dev.github.io/youthu/",
- textVersion = paste("Matthew Hamilton <[email protected]> [aut, cre] (<https://orcid.org/0000-0001-7407-9194>) and Caroline Gao <[email protected]> [aut] (<https://orcid.org/0000-0002-0987-2759>) ",
+ textVersion = paste("Matthew Hamilton <[email protected]> [aut, cre, cph] (<https://orcid.org/0000-0001-7407-9194>) and Caroline Gao <[email protected]> [aut] (<https://orcid.org/0000-0002-0987-2759>) ",
  "(2024).",
  paste0(meta$Package,": ",meta$Title,
  "."),

vignettes/Prediction_With_Mdls.Rmd

@@ -21,7 +21,8 @@ This vignette outlines a workflow for:
 - Preparing a prediction dataset for use with a selected transfer to utility model; and
 - Applying the selected transfer to utility model to a prediction dataset to predict Quality Adjusted Life Years (QALYs).
 
-The practical value of implementing such a workflow is discussed in the [economic analysis vignette](https://ready4-dev.github.io/youthu/articles/Economic_Analysis.html) and [a scientific manuscript](https://www.medrxiv.org/content/10.1101/2021.07.07.21260129v2.full). Note, this example uses fake data - it should should not be used to inform decision making.
+The practical value of implementing such a workflow is discussed in the [economic analysis vignette](https://ready4-dev.github.io/youthu/articles/Economic_Analysis.html) and [a scientific manuscript](
+https://www.medrxiv.org/content/10.1101/2021.07.07.21260129v4). Note, this example uses fake data - it should should not be used to inform decision making.
 
 ## Search, select and retrieve transfer to utility models
 To identify datasets that contain transfer to utility models compatible with youthu (ie those developped with the [TTU package](https://ready4-dev.github.io/TTU/index.html)), you can use the `get_ttu_dv_dss` function. The function searches specified dataverses (in the below example, the [TTU dataverse](https://dataverse.harvard.edu/dataverse/TTU)) for datasets containing output from the TTU package.

vignettes/V_01.Rmd

@@ -110,7 +110,6 @@ data_tb <- transform_ds_to_drop_msng(data_tb, predictors_chr = c("gad7", "phq9")
  uid_var_nm_1L_chr = "fkClientID")
 ```
 
-
 We now predict AQoL-6D health utility for each case with complete data.
 
 ```{r}

vignettes/youthu.Rmd

@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 ```{r setup}
 library(youthu)
 ```
-The tools in youthu are designed to make it easier to predict health utility with the [ready4 health economic model](https://www.ready4-dev.com/docs/model/).
+The tools in youthu are designed to make it easier to predict health utility with the [readyforwhatsnext health economic model](https://readyforwhatsnext.org/).
 
 This development version of the youthu package has been made available as part of the process of testing and documenting the package.