edits to packge description and vignette

.github/workflows/R-CMD-check.yaml

@@ -1,7 +1,4 @@
 # Adapted from: https://github.com/ready4-dev/ready4class/runs/3657635374?check_suite_focus=true
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
 #
 # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
 # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
@@ -29,85 +26,43 @@ jobs:
         config:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
-          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.0.0 (ubuntu-20.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-20.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'release'}
+          #- {os: windows-latest, r: '3.6'}
+#          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.0.0 (ubuntu-20.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+#          - {os: ubuntu-20.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          #- {os: ubuntu-20.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
-
+      - uses: actions/checkout@v3 #
       - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-
+        # with:
+        #   r-version: ${{ matrix.config.r }}
+        #   http-user-agent: ${{ matrix.config.http-user-agent }}
+        #   use-public-rspm: true
+      - uses: r-lib/actions/setup-tinytex@v2
+      - run: tlmgr --version
       - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows' && !matrix.config.autobrew
-        uses: actions/cache@v1
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
+          pandoc-version: '2.17.1' # The pandoc version to download (if necessary) and use.
+      - run: echo "# Test" | pandoc -t html
+        # Addresses issue with incompatibility between libcurl4-gnutls-dev and libcurl4-openssl-dev
+        # Below fix is a customisation of approach outlined in https://github.com/r-hub/sysreqsdb/issues/77#issuecomment-620025428
+      - name: Install libraptor on Linux
         if: runner.os == 'Linux'
         run: |
-          sudo apt-get install libharfbuzz-dev
-          sudo apt-get install libfribidi-dev
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
-      - name: Install system dependencies
-        if: runner.os == 'MacOS' && !matrix.config.autobrew
-        run: brew install harfbuzz fribidi
-
-      - name: Remove homebrew
-        if: matrix.config.autobrew
-        uses: autobrew/uninstall-homebrew@master
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+          sudo add-apt-repository ppa:cran/librdf
+          sudo apt update
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::XML, any::rcmdcheck
+          needs: check
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"error"'
+          check-dir: '"check"'

.github/workflows/pkgdown.yaml

@@ -24,12 +24,22 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - uses: r-lib/actions/setup-tinytex@v2
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
+    # Addresses issue with incompatibility between libcurl4-gnutls-dev and libcurl4-openssl-dev
+    # Below fix is a customisation of approach outlined in https://github.com/r-hub/sysreqsdb/issues/77#issuecomment-620025428
+      - name: Install libraptor on Linux
+        if: runner.os == 'Linux'
+        run: |
+          sudo add-apt-repository ppa:cran/librdf
+          sudo apt update
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::XML, any::pkgdown, local::.

DESCRIPTION

@@ -45,7 +45,8 @@ Imports:
 VignetteBuilder: knitr
 Depends: 
     R (>= 2.10),
-    specific
+    scorz (>= 0.0.0.9062),
+    specific (>= 0.0.0.9108)
 LazyData: true
 Collate: 
     'C4_TTUSynopsis.R'
@@ -71,9 +72,12 @@ Suggests:
     betareg,
     caret,
     knitrBootstrap,
-    rmarkdown
+    rmarkdown,
+    youthvars (>= 0.0.0.9123)
 Remotes: 
     ready4-dev/ready4,
     ready4-dev/ready4show,
     ready4-dev/ready4use,
-    ready4-dev/specific
+    ready4-dev/specific,
+    ready4-dev/youthvars,
+    ready4-dev/scorz

README.md

@@ -4,17 +4,20 @@
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![ready4](https://img.shields.io/badge/ready4-modelling-indigo?style=flat&labelColor=black&logo=data:image/png;base64,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)](https://www.ready4-dev.com/toolkits/)
+[![ready4](https://img.shields.io/badge/ready4-modelling-indigo?style=flat&labelColor=black&logo=data:image/png;base64,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)](https://www.ready4-dev.com/docs/software/libraries/types/module/)
 [![R-CMD-check](https://github.com/ready4-dev/TTU/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ready4-dev/TTU/actions/workflows/R-CMD-check.yaml)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5646593.svg)](https://doi.org/10.5281/zenodo.5646593)
 <!-- badges: end -->
 
-Tools for developing, reporting and sharing utility mapping
-algorithms for use with the ready4 youth mental health systems model
-(https://ready4-dev.github.io/ready4/).  This development version of
-the TTU 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]).
+Modules from the ready4 youth mental health economic model
+(https://www.ready4-dev.com/docs/model/) that can be used to develop,
+assess, report and share utility mapping models.  Outputs produced
+through use of TTU package modules are designed to integrate with
+health economic models developed with the ready4 framework
+(https://www.ready4-dev.com/).  This development version of the TTU
+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]).
 
 To install a development version of this software, run the following commands in your R console:
 

_pkgdown.yml

@@ -10,7 +10,7 @@ home:
     href: https://github.com/ready4-dev/TTU/releases/download/Documentation_0.0/TTU_User.pdf
   - text: Manual - Developer (PDF)
     href: https://github.com/ready4-dev/TTU/releases/download/Documentation_0.0/TTU_Developer.pdf
-  - text: Model
+  - text: Framework & Model
     href:  https://ready4-dev.github.io/ready4/
 development:
   mode: auto

data-raw/DATASET.R

@@ -1,3 +1,4 @@
+library(ready4)
 library(ready4fun)
 library(ready4use)
 library(ready4show)
@@ -9,7 +10,8 @@ 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 = "Implement Transfer to Utility Mapping Algorithms",
-                                                    pkg_desc_1L_chr = "Tools for developing, reporting and sharing utility mapping algorithms for use with the ready4 youth mental health systems model (https://ready4-dev.github.io/ready4/).
+                                                    pkg_desc_1L_chr = "Modules from the ready4 youth mental health economic model (https://www.ready4-dev.com/docs/model/) that can be used to develop, assess, report and share utility mapping models.
+                            Outputs produced through use of TTU package modules are designed to integrate with health economic models developed with the ready4 framework (https://www.ready4-dev.com/).
                             This development version of the TTU 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 = "Caroline",family = "Gao",email = "[email protected]", role = c("aut"),comment = c(ORCID = "0000-0002-0987-2759")),
@@ -197,6 +199,10 @@ usethis::use_dev_package("scorz",
 usethis::use_dev_package("specific",
                          type = "Depends",
                          remote = "ready4-dev/specific")
+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()
 # usethis::use_package("readr")
 # MANUAL DELETION OF TRAILING INCLUDE

vignettes/TTU.Rmd

@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 library(TTU)
 ```
 
-The tools in TTU are designed to make it easier to implement utility mapping studies for with [ready4 - an open source health economic model of the systems shaping mental health and wellbeing in young people](https://www.ready4-dev.com).
+The [ready4 framework model modules](https://www.ready4-dev.com/docs/framework/implementation/modularity/) in TTU are designed to make it easier to implement utility mapping studies for with [ready4 youth mental health economic model](https://www.ready4-dev.com/docs/model/) (or any other model developed with the [ready4 framework](https://www.ready4-dev.com)).
 
 This development version of the TTU package has been made available as part of the process of testing and documenting the package. [Installation instructions are on the package homepage](https://ready4-dev.github.io/TTU/index.html). Currently, one vignette article is available to demonstrate how to use the TTU package:
 

vignettes/V_01.Rmd

@@ -7,27 +7,27 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-Note: **This vignette uses fake data** - it is for illustrative purposes only and should not be used to inform decision making.
+Note: **This vignette uses fake data** - it is for illustrative purposes only and should not be used to inform decision making. This vignette outlines the workflow for developing utility mapping models using longitudinal data. The workflow for developing utility mapping models is broadly similar, with some minor modifications. An example of developing models using cross-sectional data is available at https://doi.org/10.5281/zenodo.8098595 .
 
 ## Motivation
 
-Youth mental health services do not typically collect health utility data from their clients, which makes it more difficult to place an economic values on outcomes attained in these services. One strategy for addressing this gap is to use data from similar samples of young people that contain both health utility and the types of outcome measures that are collected in clinical services. The TTU package provides a toolkit for conducting and reporting a utility mapping (or Transfer to Utility) study.
+Health services do not typically collect health utility data from their clients, which makes it more difficult to place an economic values on outcomes attained in these services. One strategy for addressing this gap is to use data from similar samples of patients that contain both health utility and the types of outcome measures that are collected in clinical services. The TTU package provides a toolkit for conducting and reporting a utility mapping (or Transfer to Utility) study.
 
 ## Implementation
+The TTU package contains [modules](https://www.ready4-dev.com/docs/framework/implementation/modularity/) of the [ready4 youth mental health economic model](https://www.ready4-dev.com/docs/model/) that combine and extend model modules for:
 
-TTU has been developed for use with the [ready4 model](https://ready4-dev.github.io/ready4/) and combines and extends multiple types of [ready4 modules](https://ready4-dev.github.io/ready4/articles/V_01.html):
-
-- Modules for labeling, validating and summarising youth mental health datasets from the [youthvars](https://ready4-dev.github.io/youthvars/) package;
-- Modules for scoring health utility from the [scorz](https://ready4-dev.github.io/scorz/) package;
-- Modules for specifying and testing statistical models from the [specific](https://ready4-dev.github.io/specific/) package;
-- Modules for generating reports from the [ready4show](https://ready4-dev.github.io/ready4show/) package; and
-- Modules for sharing data via online data repositories from the [ready4use](https://ready4-dev.github.io/ready4use/) package.
+- labeling, validating and summarising youth mental health datasets (from the [youthvars](https://ready4-dev.github.io/youthvars/) package);
+- scoring health utility (from the [scorz](https://ready4-dev.github.io/scorz/) package);
+- specifying and testing statistical models (from the [specific](https://ready4-dev.github.io/specific/) package);
+- generating reproducible analysis reports (from the [ready4show](https://ready4-dev.github.io/ready4show/) package); and
+- sharing data via online data repositories (from the [ready4use](https://ready4-dev.github.io/ready4use/) package).
 
 Additionally, TTU relies on two RMarkdown programs:
 
 - ttu_mdl_ctlg: Generate a Template Utility Mapping (Transfer to Utility) Model Catalogue (https://doi.org/10.5281/zenodo.5936870)
 - ttu_lng_ss: Create a Draft Scientific Manuscript For A Utility Mapping Study (https://doi.org/10.5281/zenodo.5976987)
 
+Outputs generated by the TTU package are designed to be compatible with health economic models developed with the [ready4 framework](https://www.ready4-dev.com)).
 
 ## Workflow
 ### Background and citation 
@@ -108,7 +108,7 @@ A <- Ready4useDyad(ds_tb = Ready4useRepos(dv_nm_1L_chr = "fakes", dv_ds_nm_1L_ch
   renew(type_1L_chr = "label")
 ```
 
-We use the YouthvarsSeries module to [supply metadata about out a longitudinal dataset vignette](https://ready4-dev.github.io/youthvars/articles/V_02.html).
+We use the YouthvarsSeries module to [supply metadata about our longitudinal dataset vignette](https://ready4-dev.github.io/youthvars/articles/V_02.html).
 
 ```{r}
 A <- YouthvarsSeries(a_Ready4useDyad = A, id_var_nm_1L_chr = "fkClientID", timepoint_var_nm_1L_chr = "round",