From 99478a4913e4fc417efaec8508c86bf9a2e00802 Mon Sep 17 00:00:00 2001 From: Matthew P Hamilton <30450935+matthewphamilton@users.noreply.github.com> Date: Wed, 4 Oct 2023 15:14:13 +1100 Subject: [PATCH] edits to packge description and vignette --- .DS_Store | Bin 0 -> 6148 bytes ._.DS_Store | Bin 0 -> 4096 bytes .github/workflows/R-CMD-check.yaml | 99 ++++++++--------------------- .github/workflows/pkgdown.yaml | 10 +++ DESCRIPTION | 10 ++- README.md | 17 +++-- _pkgdown.yml | 2 +- data-raw/DATASET.R | 8 ++- data/mdl_types_lup.rda | Bin 869 -> 874 bytes data/plt_types_lup.rda | Bin 483 -> 480 bytes data/rprt_lup.rda | Bin 468 -> 462 bytes man/TTU-package.Rd | 4 +- vignettes/TTU.Rmd | 2 +- vignettes/V_01.Rmd | 20 +++--- 14 files changed, 75 insertions(+), 97 deletions(-) create mode 100644 .DS_Store create mode 100644 ._.DS_Store diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..2844a403864b99d26a6c347efaac19dc893d7f35 GIT binary patch literal 6148 zcmeHKu}T9$5S=xLL{BiKb|(m85kc?+&TxXQrqjm6NK_IpXrk?b*a#L@_SOo1fmkSl zKVYl)5w^bB-IzTt(N0umVD|0p%LZd7=Ul<)Mt;D4IUPcGipx*%1y_ zJV&EGU*3$Ht&FD(2m`{vZ)8A!_%ug#+M%}l{XR~eT_ItwYiq_)RBgmnjOCwJZa3Cv z9v0K~+L!j$cJFL>e11VF`Ivi^TC`6w?V{hI1KOf}Hw*PX_Bz$Vqox1Ojhs@R)|o50+1L3ClDJkFz{^v(m+1nBL)UWIhYCu0iY;W;207T zWIgNTe~1o-3apAo1xG_*Gz3ONU^E0qLtr!nMnhmU1V%$(Gz3ONU^E0qLx9R5zz8%C zguy^ABqOs}p(wRDzqBYhRUs|EC|e;juOv0EBr`uRF(;=|AtyDhL?J0BF)tg~)rIOB Q(iE!y;a-tpko*510KSwTa{vGU literal 0 HcmV?d00001 diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 3ad15665..9a6ecbbe 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.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 @@ -29,10 +26,11 @@ 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 @@ -40,74 +38,31 @@ jobs: 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"' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 23151085..a53dec9f 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.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::. diff --git a/DESCRIPTION b/DESCRIPTION index 553a0085..fdc8d41d 100644 --- a/DESCRIPTION +++ b/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 diff --git a/README.md b/README.md index 12b35bf3..07486cdc 100644 --- a/README.md +++ b/README.md @@ -4,17 +4,20 @@ [![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) -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 (matthew.hamilton1@monash.edu). +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 (matthew.hamilton1@monash.edu). To install a development version of this software, run the following commands in your R console: diff --git a/_pkgdown.yml b/_pkgdown.yml index 36a18147..b2f59470 100644 --- a/_pkgdown.yml +++ b/_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 diff --git a/data-raw/DATASET.R b/data-raw/DATASET.R index e05b411e..16d69eac 100644 --- a/data-raw/DATASET.R +++ b/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 (matthew.hamilton1@monash.edu).", authors_prsn = c(utils::person(given = "Caroline",family = "Gao",email = "caroline.gao@orygen.org.au", 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 diff --git a/data/mdl_types_lup.rda b/data/mdl_types_lup.rda index 3fcb7de0dc6fd7ff7dcd6f2cb430b4ffcaa9f357..f8d0a70622e5934ef5955bca6e78a71bf681c46a 100644 GIT binary patch delta 861 zcmV-j1ET!p2I>Y5LRx4!F+o`-Q(5{D+-i{y9Dg^pU6Nr`A(ClH>S?qlhp5oR(9wt) zGe|UKz>Fr;ex%3|5_+Derbq#ilRy9iKn8#S0084AO&SA6n2e1KLjq{i5MneKKmmd& zDdeX05^YZ!Mx*slNr-4PXwc9GjDP{4+CdakRPvsg6GZfBsA$tbGy^~~XwWoh8fl}- zXnz!#!zBXy(-t`ZErkNhSYbAxUFtIcY1j`g#L#N`?(y#%nag+E@-gG zmR}+SA%r!T8ZP`8M{%G3L{Y^@D9KjRLumm z5cmSXbEH_1GTTJKgiVtVka-?w6Mu1zMSypC^+S4m?)R+K41o&*Lc4q_7iCL@$zExJ z`jRRE)k&$&t@Lu-*Nh6IyBP(=iw>lM@e80BSYXvq(%vrZ5U{>*JQ~r>I+1L*eKEgo$>7U@o17z2IU40LRx4!F+o`-Q(5}klQ`GVx0Lh>L0000000425CXE53Oh!hAA%Qe$h%p)rAOOJ? z6!b++)CiP z(42v(&yqul$j47>oXS#>O)aDBE4=n0UFsYAvbyBn+p@eiR2hy{ZwAo#)a4ejF95&} z#D(;L#i~hO5iT(6ADhhLY%)Yx1Ap88Wev)1yPlJt7{V+PE1P{o7DU7@J9X&?@KCq| zq>@wot^{~p)eQrnG%aIVkT0c>6I;#=R`X~$XOv5(=TU+f{#@%NpO7O+uCaeU>T;SEkbdnw4iKVO#PWZn1zYh65(zP?tnV9 ix`np_?O3iwFV;=p=kyRzNNuS9#oUoj6eK>qhtz-opnAsu diff --git a/data/plt_types_lup.rda b/data/plt_types_lup.rda index dc25b9863d1aebd0ab38ff9492f16968b9c3365d..ce1723f679de6da9bf44b1e1b72954dd67ad849b 100644 GIT binary patch delta 445 zcmV;u0Yd)c1Kp!d{`f)t&At9rL_;Y$eD&F!<<=?v zZc{rV+hkr@FnB^DVG*)Q6AH~HAqT9#S%hkp=TD@}%61hhW^R47u-;aaDVg9mn+lXF zS~eRCMTNyni+>KK2C;{}eLQpH(vh{7-*n@a{FXIEQSL0zk!i5`g+~y>WG3>#)WK=Q zUVWb3KbWUKj=lQ!{CD^x6Pg|*l1G8S^w3b#SsyAzr#~ail8E+Dc^gQ*g^w~l4^z;M z;|F1(uA{asmfx^>b#9*NSG2x?Q#>Vet&0!-h~N|p!~R=C1X)2NYGH3 zB-G*UU|w7`)RH8`%*4pRa}}USx*Vj8xg6{?I9yFkl^2VS^eSlZ?`dHgXN=DR6lI{+ zRG^a*Ej<6qT!)Vus0YFV1Ngg=DZ+$-9mAlY7F*I# delta 448 zcmV;x0YCoW1LFe@LRx4!F+o`-Q&~r#Ca#eV9|T)~07j896n_mhAZjvX(U8y?83&{p zG|7Ufg&8sp8km%Lpz@E@nj6$GPSHPNJnujjyJ5HGGWGZZt@NApOy=j3^kQ69<xZ^-a_(4jH&AD0uvtY{?( z8Hy7mnjAf>7#EE-B#AZ|8x6)In5_au@Z}_KfEE(Uul(QQap&9Mo!bnXgk`;-YjJ!UnxxOG#u@wA71$zp#04c q@*+m^gdv*BDsI4X+EQ*JNf(WS1)-1MssE5c#9hf0;X*+kfSS09Ptvvk diff --git a/data/rprt_lup.rda b/data/rprt_lup.rda index 31cedb630ff1abff2c013f8158257cfaa51c2c0f..383ae503fcef085dd966be9259cf82f0668fc864 100644 GIT binary patch delta 446 zcmV;v0YU!M1I_~uLRx4!F+o`-Q(33LT04;r9DlU5hKinQOpO^005kvwng9R*&}c$v z$jUt?nuFAOfB~QbKmheUK_rAsi1jvVk0g3P00w}_8USref#HIRK+_2(a*P}&&E~_> z_+s4ehFY?6NiZ3%(KwgO1YW+TdwUA>HOoR_$ zaDOs;0Ok@AnbCFLA01M%Nu~_*O`OAO6K)3 z;n+#1$<;1>8>;twdu#M)_@~*Tm+z6V1sDkDyCt~_&zHD(K5gE*89T77{W22;xV0%` zV+Z=2H-U-o+#j`%eAJV}^71B#)BDC@~ ztn^^d>}(auZU6uP delta 452 zcmV;#0XzQA1JnZ!LRx4!F+o`-Q(11D0c?>D9DjgAL^LLYLrIdGDdirf)CToWP|YTX zqbT(ro~Uz1OiTbwMg(br1|tN?fJO-vO;PGJ$)}{zlMv7WrbbON4FRKSQV|N3w*aaV zo(ja!6le5gQu$@g5u3`4T~eG3)auwpR)gt{PcoiU+*oyR5et?MJiW8O_N>{sA$^59_g z_%XgFKK-Px56mfJ@%Ar_@$Q!g4pezKQ9jZ%0cHZBcNEzL{X01ehNGizSb6pCVe@!T zcFen0!M&&F=-sp!yvNOJVMZ%>Nrr+fe1CTVsN2?km8(}egqWH1a1aTw5ZNN*|!tuy*&>Z_wzQXzeT zxMvrV#IGyn=$>kEP)#R?PDIITV(_$BSyVaijP4N!4Q9(lBH^0Ws?n!O+L9+`X)P#| u9F %\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",