data-raw/DATASET.R
In ready4-dev/scorz: Score Multi-Attribute Utility Instruments
library(ready4)
library(ready4fun)
library(ready4show)
library(ready4use)
library(youthvars)
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 = "Score Multi-Attribute Utility Instruments" %>% tools::toTitleCase(),
pkg_desc_1L_chr = "Modules from the readyforwhatsnext youth mental health economic model (https://readyforwhatsnext.org/) that can be used to summarise multiple questionnaire responses in a single index measure.
This package uses publicly available scoring algorithms to calculate health utility from multi-attribute utility instruments and has been developed with the ready4 framework (https://www.ready4-dev.com/).
This development version of the scorz 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 = "Matthew",family = "Hamilton",email = "matthew.hamilton1@monash.edu", role = c("aut", "cre", "cph"),comment = c(ORCID = "0000-0001-7407-9194")),
utils::person(given = "Caroline",family = "Gao",email = "caroline.gao@orygen.org.au", role = c("aut"),comment = c(ORCID = "0000-0002-0987-2759")),
utils::person("Orygen", role = c("cph", "fnd")),
utils::person("Headspace", role = c( "fnd")),
utils::person("National Health and Medical Research Council", role = c( "fnd"))),
urls_chr = c("https://ready4-dev.github.io/scorz/",
"https://github.com/ready4-dev/scorz",
"https://www.ready4-dev.com/")) %>%
ready4fun::make_manifest(addl_pkgs_ls = ready4fun::make_addl_pkgs_ls(depends_chr = "ready4",
suggests_chr = "rmarkdown",
imports_chr = "knitrBootstrap"),
build_ignore_ls = ready4fun::make_build_ignore_ls(file_nms_chr = c("initial_setup.R")),
check_type_1L_chr = "ready4",
copyright_holders_chr = "Matthew Hamilton and Orygen",
custom_dmt_ls = ready4fun::make_custom_dmt_ls(#user_manual_fns_chr = c()
),##
dev_pkgs_chr = c(#"ready4",
"ready4use","ready4show",
"youthvars"),
lifecycle_stage_1L_chr = "experimental",
path_to_pkg_logo_1L_chr = "../../../../../Documentation/Images/scorz-logo/default.png",
piggyback_to_1L_chr = "ready4-dev/ready4",
ready4_type_1L_chr = "description",
zenodo_badge_1L_chr = "[](https://doi.org/10.5281/zenodo.5722708)"
)
y <- dplyr::bind_rows(ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Profile",
slots_ls = list("a_YouthvarsProfile",
"country_1L_chr",
"domain_unwtd_var_nms_chr",
"domain_wtd_var_nms_chr",
"instrument_dict_r3",
"instrument_nm_1L_chr",
"instrument_short_nm_1L_chr",
"instrument_version_1L_chr",
"itm_labels_chr",
"itm_prefix_1L_chr",
"scrg_dss_ls",
"total_wtd_var_nm_1L_chr",
"total_unwtd_var_nm_1L_chr"
) %>% list(),
pt_ls = list("YouthvarsProfile",
"character",
"character",
"character",
"ready4use_dictionary",
"character",
"character",
"character",
"character",
"character",
"list",
"character",
"character") %>% list(),
class_desc_chr= "A dataset to be scored, its associated metadata and details of the scoring instrument.",
parent_class_chr = "Ready4Module"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Aqol6",
slots_ls = list("a_YouthvarsProfile",
"country_1L_chr",
"domain_unwtd_var_nms_chr",
"domain_wtd_var_nms_chr",
"instrument_dict_r3",
"instrument_nm_1L_chr",
"instrument_short_nm_1L_chr",
"instrument_version_1L_chr",
"itm_labels_chr",
"itm_prefix_1L_chr",
"scrg_dss_ls",
"total_wtd_var_nm_1L_chr",
"total_unwtd_var_nm_1L_chr"
) %>% list(),
pt_ls = list("YouthvarsProfile",
"character",
"character",
"character",
"ready4use_dictionary",
"character",
"character",
"character",
"character",
"character",
"list",
"character",
"character") %>% list(),
vals_ls = list(list(domain_wtd_var_nms_chr = "paste0(\"vD\",1:6)",
instrument_dict_r3 = " make_aqol6d_scrg_dict()",
instrument_nm_1L_chr = "'Assessment of Quality of Life (6 Dimension)'",
instrument_short_nm_1L_chr = "'AQoL-6D'",
#instrument_version_1L_chr = NA_character_,
itm_labels_chr = "make_aqol6d_item_nms()",
itm_prefix_1L_chr = "'aqol6d_q'",
scrg_dss_ls = "make_aqol6d_scrg_dss()",
total_wtd_var_nm_1L_chr = "'aqol6d_total_w'",
total_unwtd_var_nm_1L_chr = "'aqol6d_total_c'"
)),
class_desc_chr = "A dataset and metadata to support implementation of an AQoL-6D scoring algorithm.",
parent_class_chr = "ScorzProfile"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Aqol6Adol",
slots_ls = list("instrument_version_1L_chr") %>% list(),
pt_ls = list("character") %>% list(),
vals_ls = list(list(instrument_version_1L_chr = "'Adolescent'")),
class_desc_chr = "A dataset and metadata to support implementation of a scoring algorithm for the adolescent version of AQoL-6D.",
parent_class_chr = "ScorzAqol6"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Aqol6Adult",
slots_ls = list("instrument_version_1L_chr") %>% list(),
pt_ls = list("character") %>% list(),
vals_ls = list(list(instrument_version_1L_chr = "'Adult'")),
class_desc_chr = "A dataset and metadata to support implementation of a scoring algorithm for the adult version of AQoL-6D.",
parent_class_chr = "ScorzAqol6"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "EuroQol5",
slots_ls = list("a_YouthvarsProfile",
"country_1L_chr",
"domain_unwtd_var_nms_chr",
"domain_wtd_var_nms_chr",
"instrument_dict_r3",
"instrument_nm_1L_chr",
"instrument_short_nm_1L_chr",
"instrument_version_1L_chr",
"itm_labels_chr",
"itm_prefix_1L_chr",
"itm_var_nms_chr",
"scrg_dss_ls",
"total_wtd_var_nm_1L_chr",
"total_unwtd_var_nm_1L_chr",
"type_1L_chr"
) %>% list(),
pt_ls = list("YouthvarsProfile",
"character",
"character",
"character",
"ready4use_dictionary",
"character",
"character",
"character",
"character",
"character",
"character",
"list",
"character",
"character",
"character") %>% list(),
vals_ls = list(list(domain_wtd_var_nms_chr = "c(\"eq5dq_MO\", \"eq5dq_SC\", \"eq5dq_UA\", \"eq5dq_PD\", \"eq5dq_AD\")",
instrument_dict_r3 = "make_eq5d_dict()",
instrument_nm_1L_chr = "'EuroQol EQ-5D'",
#instrument_version_1L_chr = NA_character_,
itm_labels_chr = "c(\"Mobility\", \"Self-care\", \"Usual Activities\",\"Pain-Discomfort\",\"Anxiety-Depression\")",
itm_prefix_1L_chr = "'eq5dq_'",
itm_var_nms_chr = "c(\"eq5dq_MO\", \"eq5dq_SC\", \"eq5dq_UA\", \"eq5dq_PD\", \"eq5dq_AD\")",
#scrg_dss_ls = "make_aqol6d_scrg_dss()",
total_wtd_var_nm_1L_chr = "'eq5d_total_w'",
total_unwtd_var_nm_1L_chr = "'eq5d_total_c'",
type_1L_chr = "'CW'"
)),
class_desc_chr = "A dataset and metadata to support implementation of an EQ-5D scoring algorithm.",
parent_class_chr = "ScorzProfile")) %>%
ready4class::ready4class_constructor()
aqol6d_scrg_dss_ls <- fns_env_ls$fns_env$get_aqol6d_scrg_dss()
datasets_ls <- list(
aqol6d_scrg_dss_ls$aqol6d_adult_vldn_pop_with_STATA_scores_tb %>%
ready4fun::make_pkg_ds_ls(db_1L_chr = "aqol6d_adult_vldn_pop_with_STATA_scores_tb",
title_1L_chr = "STATA comparison validation synthetic population",
desc_1L_chr = "Synthetic population following application of STATA adult scoring algorithm.",
url_1L_chr = "https://www.aqol.com.au/index.php/scoring-algorithms"),
aqol6d_scrg_dss_ls$adol_dim_sclg_eqs_lup %>%
ready4fun::make_pkg_ds_ls(db_1L_chr = "adol_dim_sclg_eqs_lup",
title_1L_chr = "AQoL6D (adolescent) item worst weightings equations lookup table",
desc_1L_chr = "Dimension scaling equations for adolescent version of AQoL6D scoring algorithm.",
url_1L_chr = "https://www.aqol.com.au/index.php/scoring-algorithms"))
z <- ready4pack::make_pt_ready4pack_manifest(x,
constructor_r3 = y,
pkg_ds_ls_ls = datasets_ls) %>%
ready4pack::ready4pack_manifest()
z <- ready4::author(z)
write_to_edit_workflow("pkgdown.yaml", consent_1L_chr = "Y") # In other packages, run for "test-coverage.yaml" as well.
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")
paste0(".github/workflows/", c("pkgdown.yaml", "R-CMD-check.yaml")) %>%
purrr::walk(~{
path_1L_chr <- .x
matches_int <- which(readLines(path_1L_chr) %>% startsWith(" # Addresses issue with incompatibility between libcurl4-gnutls-dev and libcurl4-openssl-dev") | readLines(path_1L_chr) %>% startsWith(" # Addresses issue with incompatibility between libcurl4-gnutls-dev and libcurl4-openssl-dev"))
if(!identical(matches_int,integer(0))){
readLines(path_1L_chr)[- (matches_int%>%
purrr::map(~.x:(.x+6)) %>% purrr::flatten_int())] %>%
writeLines(path_1L_chr)
}
})
ready4-dev/scorz documentation built on June 1, 2025, 2:07 p.m.
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library(ready4)
library(ready4fun)
library(ready4show)
library(ready4use)
library(youthvars)
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 = "Score Multi-Attribute Utility Instruments" %>% tools::toTitleCase(),
pkg_desc_1L_chr = "Modules from the readyforwhatsnext youth mental health economic model (https://readyforwhatsnext.org/) that can be used to summarise multiple questionnaire responses in a single index measure.
This package uses publicly available scoring algorithms to calculate health utility from multi-attribute utility instruments and has been developed with the ready4 framework (https://www.ready4-dev.com/).
This development version of the scorz 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 = "Matthew",family = "Hamilton",email = "matthew.hamilton1@monash.edu", role = c("aut", "cre", "cph"),comment = c(ORCID = "0000-0001-7407-9194")),
utils::person(given = "Caroline",family = "Gao",email = "caroline.gao@orygen.org.au", role = c("aut"),comment = c(ORCID = "0000-0002-0987-2759")),
utils::person("Orygen", role = c("cph", "fnd")),
utils::person("Headspace", role = c( "fnd")),
utils::person("National Health and Medical Research Council", role = c( "fnd"))),
urls_chr = c("https://ready4-dev.github.io/scorz/",
"https://github.com/ready4-dev/scorz",
"https://www.ready4-dev.com/")) %>%
ready4fun::make_manifest(addl_pkgs_ls = ready4fun::make_addl_pkgs_ls(depends_chr = "ready4",
suggests_chr = "rmarkdown",
imports_chr = "knitrBootstrap"),
build_ignore_ls = ready4fun::make_build_ignore_ls(file_nms_chr = c("initial_setup.R")),
check_type_1L_chr = "ready4",
copyright_holders_chr = "Matthew Hamilton and Orygen",
custom_dmt_ls = ready4fun::make_custom_dmt_ls(#user_manual_fns_chr = c()
),##
dev_pkgs_chr = c(#"ready4",
"ready4use","ready4show",
"youthvars"),
lifecycle_stage_1L_chr = "experimental",
path_to_pkg_logo_1L_chr = "../../../../../Documentation/Images/scorz-logo/default.png",
piggyback_to_1L_chr = "ready4-dev/ready4",
ready4_type_1L_chr = "description",
zenodo_badge_1L_chr = "[](https://doi.org/10.5281/zenodo.5722708)"
)
y <- dplyr::bind_rows(ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Profile",
slots_ls = list("a_YouthvarsProfile",
"country_1L_chr",
"domain_unwtd_var_nms_chr",
"domain_wtd_var_nms_chr",
"instrument_dict_r3",
"instrument_nm_1L_chr",
"instrument_short_nm_1L_chr",
"instrument_version_1L_chr",
"itm_labels_chr",
"itm_prefix_1L_chr",
"scrg_dss_ls",
"total_wtd_var_nm_1L_chr",
"total_unwtd_var_nm_1L_chr"
) %>% list(),
pt_ls = list("YouthvarsProfile",
"character",
"character",
"character",
"ready4use_dictionary",
"character",
"character",
"character",
"character",
"character",
"list",
"character",
"character") %>% list(),
class_desc_chr= "A dataset to be scored, its associated metadata and details of the scoring instrument.",
parent_class_chr = "Ready4Module"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Aqol6",
slots_ls = list("a_YouthvarsProfile",
"country_1L_chr",
"domain_unwtd_var_nms_chr",
"domain_wtd_var_nms_chr",
"instrument_dict_r3",
"instrument_nm_1L_chr",
"instrument_short_nm_1L_chr",
"instrument_version_1L_chr",
"itm_labels_chr",
"itm_prefix_1L_chr",
"scrg_dss_ls",
"total_wtd_var_nm_1L_chr",
"total_unwtd_var_nm_1L_chr"
) %>% list(),
pt_ls = list("YouthvarsProfile",
"character",
"character",
"character",
"ready4use_dictionary",
"character",
"character",
"character",
"character",
"character",
"list",
"character",
"character") %>% list(),
vals_ls = list(list(domain_wtd_var_nms_chr = "paste0(\"vD\",1:6)",
instrument_dict_r3 = " make_aqol6d_scrg_dict()",
instrument_nm_1L_chr = "'Assessment of Quality of Life (6 Dimension)'",
instrument_short_nm_1L_chr = "'AQoL-6D'",
#instrument_version_1L_chr = NA_character_,
itm_labels_chr = "make_aqol6d_item_nms()",
itm_prefix_1L_chr = "'aqol6d_q'",
scrg_dss_ls = "make_aqol6d_scrg_dss()",
total_wtd_var_nm_1L_chr = "'aqol6d_total_w'",
total_unwtd_var_nm_1L_chr = "'aqol6d_total_c'"
)),
class_desc_chr = "A dataset and metadata to support implementation of an AQoL-6D scoring algorithm.",
parent_class_chr = "ScorzProfile"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Aqol6Adol",
slots_ls = list("instrument_version_1L_chr") %>% list(),
pt_ls = list("character") %>% list(),
vals_ls = list(list(instrument_version_1L_chr = "'Adolescent'")),
class_desc_chr = "A dataset and metadata to support implementation of a scoring algorithm for the adolescent version of AQoL-6D.",
parent_class_chr = "ScorzAqol6"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Aqol6Adult",
slots_ls = list("instrument_version_1L_chr") %>% list(),
pt_ls = list("character") %>% list(),
vals_ls = list(list(instrument_version_1L_chr = "'Adult'")),
class_desc_chr = "A dataset and metadata to support implementation of a scoring algorithm for the adult version of AQoL-6D.",
parent_class_chr = "ScorzAqol6"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "EuroQol5",
slots_ls = list("a_YouthvarsProfile",
"country_1L_chr",
"domain_unwtd_var_nms_chr",
"domain_wtd_var_nms_chr",
"instrument_dict_r3",
"instrument_nm_1L_chr",
"instrument_short_nm_1L_chr",
"instrument_version_1L_chr",
"itm_labels_chr",
"itm_prefix_1L_chr",
"itm_var_nms_chr",
"scrg_dss_ls",
"total_wtd_var_nm_1L_chr",
"total_unwtd_var_nm_1L_chr",
"type_1L_chr"
) %>% list(),
pt_ls = list("YouthvarsProfile",
"character",
"character",
"character",
"ready4use_dictionary",
"character",
"character",
"character",
"character",
"character",
"character",
"list",
"character",
"character",
"character") %>% list(),
vals_ls = list(list(domain_wtd_var_nms_chr = "c(\"eq5dq_MO\", \"eq5dq_SC\", \"eq5dq_UA\", \"eq5dq_PD\", \"eq5dq_AD\")",
instrument_dict_r3 = "make_eq5d_dict()",
instrument_nm_1L_chr = "'EuroQol EQ-5D'",
#instrument_version_1L_chr = NA_character_,
itm_labels_chr = "c(\"Mobility\", \"Self-care\", \"Usual Activities\",\"Pain-Discomfort\",\"Anxiety-Depression\")",
itm_prefix_1L_chr = "'eq5dq_'",
itm_var_nms_chr = "c(\"eq5dq_MO\", \"eq5dq_SC\", \"eq5dq_UA\", \"eq5dq_PD\", \"eq5dq_AD\")",
#scrg_dss_ls = "make_aqol6d_scrg_dss()",
total_wtd_var_nm_1L_chr = "'eq5d_total_w'",
total_unwtd_var_nm_1L_chr = "'eq5d_total_c'",
type_1L_chr = "'CW'"
)),
class_desc_chr = "A dataset and metadata to support implementation of an EQ-5D scoring algorithm.",
parent_class_chr = "ScorzProfile")) %>%
ready4class::ready4class_constructor()
aqol6d_scrg_dss_ls <- fns_env_ls$fns_env$get_aqol6d_scrg_dss()
datasets_ls <- list(
aqol6d_scrg_dss_ls$aqol6d_adult_vldn_pop_with_STATA_scores_tb %>%
ready4fun::make_pkg_ds_ls(db_1L_chr = "aqol6d_adult_vldn_pop_with_STATA_scores_tb",
title_1L_chr = "STATA comparison validation synthetic population",
desc_1L_chr = "Synthetic population following application of STATA adult scoring algorithm.",
url_1L_chr = "https://www.aqol.com.au/index.php/scoring-algorithms"),
aqol6d_scrg_dss_ls$adol_dim_sclg_eqs_lup %>%
ready4fun::make_pkg_ds_ls(db_1L_chr = "adol_dim_sclg_eqs_lup",
title_1L_chr = "AQoL6D (adolescent) item worst weightings equations lookup table",
desc_1L_chr = "Dimension scaling equations for adolescent version of AQoL6D scoring algorithm.",
url_1L_chr = "https://www.aqol.com.au/index.php/scoring-algorithms"))
z <- ready4pack::make_pt_ready4pack_manifest(x,
constructor_r3 = y,
pkg_ds_ls_ls = datasets_ls) %>%
ready4pack::ready4pack_manifest()
z <- ready4::author(z)
write_to_edit_workflow("pkgdown.yaml", consent_1L_chr = "Y") # In other packages, run for "test-coverage.yaml" as well.
write_to_tidy_pkg(z$x_ready4fun_manifest, build_vignettes_1L_lgl = TRUE,
clean_license_1L_lgl = TRUE, consent_1L_chr = "Y",
examples_chr = character(0),
suggest_chr = "pkgload")
paste0(".github/workflows/", c("pkgdown.yaml", "R-CMD-check.yaml")) %>%
purrr::walk(~{
path_1L_chr <- .x
matches_int <- which(readLines(path_1L_chr) %>% startsWith(" # Addresses issue with incompatibility between libcurl4-gnutls-dev and libcurl4-openssl-dev") | readLines(path_1L_chr) %>% startsWith(" # Addresses issue with incompatibility between libcurl4-gnutls-dev and libcurl4-openssl-dev"))
if(!identical(matches_int,integer(0))){
readLines(path_1L_chr)[- (matches_int%>%
purrr::map(~.x:(.x+6)) %>% purrr::flatten_int())] %>%
writeLines(path_1L_chr)
}
})
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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