data-raw/DATASET.R
In ready4-dev/ready4show: Author Health Economic Analysis Programs and Reporting Templates
library(ready4)
library(ready4fun)
x <- ready4fun::make_pkg_desc_ls(pkg_title_1L_chr = "Author Health Economic Analysis Programs and Reporting Templates" %>% tools::toTitleCase(),
pkg_desc_1L_chr = "ready4show provides tools for authoring repeatable analyses and to help automate the generation of scientific summaries for modelling studies implemented with the ready4 framework.
For detailed documentation about the framework and how to 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>.
This development version of the ready4show 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("Glen", "Wiesner", #email = "Glen.Wiesner@vu.edu.au",
role = c("aut"), comment = c(ORCID = "0000-0002-0071-130X")),
utils::person("Orygen", role = c("cph", "fnd")),
utils::person("Australian Government Research Training Program", role =c("fnd")),
utils::person("VicHealth",role = c("fnd")),
utils::person("Victoria University", role =c("fnd"))
),
urls_chr = c("https://ready4-dev.github.io/ready4show/",
"https://github.com/ready4-dev/ready4show",
"https://www.ready4-dev.com/")) %>%
ready4fun::make_manifest(addl_pkgs_ls = ready4fun::make_addl_pkgs_ls(#depends_chr = "ready4",
imports_chr = "knitrBootstrap",
suggests_chr = c("bookdown", "officedown","rmarkdown", "rticles")),
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("make_eq_ref","make_rprt_type_ls",
"print_table",
"write_mdl_plt_fl","write_mkdn_from_pkg","write_rprt")),
#dev_pkgs_chr = c("ready4"),
lifecycle_stage_1L_chr = "experimental",
path_to_pkg_logo_1L_chr = "../../../../../Documentation/Images/ready4show-logo/default.png",
piggyback_to_1L_chr = "ready4-dev/ready4",
ready4_type_1L_chr = "authoring",
zenodo_badge_1L_chr = "[](https://doi.org/10.5281/zenodo.5644568)")
y <- ready4class::ready4class_constructor() %>%
dplyr::bind_rows(ready4class::make_pt_ready4class_constructor(make_s3_lgl = TRUE,
name_stub_chr = "authors",
pt_ls = list(list("tibble")),
pt_chkr_pfx_ls = list(list("is_")),
pt_ns_ls = list(list("tibble")),
vals_ls = list(list(first_nm_chr = "character(0)",
middle_nm_chr = "character(0)",
last_nm_chr = "character(0)",
title_chr = "character(0)",
qualifications_chr = "character(0)",
institute_chr = "character(0)",
sequence_int = "integer(0)",
is_corresponding_lgl = "logical(0)",
email_chr = "character(0)",
is_equal_first_lgl = "logical(0)")),
class_desc_chr = "Authors lookup table"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = TRUE,
name_stub_chr = "institutes",
pt_ls = list(list("tibble")),
pt_chkr_pfx_ls = list(list("is_")),
pt_ns_ls = list(list("tibble")),
vals_ls = list(list(short_name_chr = "character(0)",
long_name_chr = "character(0)")),
class_desc_chr = "Institutes lookup table"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = TRUE,
name_stub_chr = "correspondences",
pt_ls = list(list("tibble")),
pt_chkr_pfx_ls = list(list("is_")),
pt_ns_ls = list(list("tibble")),
vals_ls = list(list(old_nms_chr = "character(0)",
new_nms_chr = "character(0)")),
class_desc_chr = "Name correspondences lookup table"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Paths",
slots_ls = list("mkdn_data_dir_1L_chr",
"mkdn_source_dir_1L_chr",
"ms_mkdn_dir_1L_chr",
"ms_dir_1L_chr",
"outp_data_dir_1L_chr",
"reports_dir_1L_chr") %>% list(),
pt_ls = list("character",
"character",
"character",
"character",
"character",
"character") %>% list(),
# vals_ls = list(list(mkdn_data_dir_1L_chr = "'Markdown'",
# ms_mkdn_dir_1L_chr = "'Manuscript'",
# ms_dir_1L_chr = "'Manuscript'",
# outp_data_dir_1L_chr = "'Output'",
# reports_dir_1L_chr = "'Reports'")),
class_desc_chr= "Metadata about paths to Markdown input and output",
parent_class_chr = "Ready4Module"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Synopsis",
slots_ls = list("a_Ready4showPaths",
"abstract_args_ls",
"authors_r3",
"background_1L_chr",
"coi_1L_chr",
"conclusion_1L_chr",
"correspondences_r3",
"digits_int",
"ethics_1L_chr",
"fl_nm_1L_chr",
"figures_in_body_lgl",
"funding_1L_chr",
"institutes_r3",
"interval_chr",
"keywords_chr",
"outp_formats_chr",
"rmd_fl_nms_ls",
"sample_desc_1L_chr",
"tables_in_body_lgl",
"title_1L_chr") %>% list(),
pt_ls = list("Ready4showPaths",
"list",
"ready4show_authors",
"character",
"character",
"character",
"ready4show_correspondences",
"integer",
"character",
"character",
"logical",
"character",
"ready4show_institutes",
"character",
"character",
"character",
"list",
"character",
"logical",
"character") %>% list(),
vals_ls = list(list(a_Ready4showPaths = "make_default_paths()",
abstract_args_ls = "make_abstract_args_ls()",
coi_1L_chr = "'None declared.'",
digits_int = "3L",
ethics_1L_chr = "'Details on ethics approvals go here.'",
figures_in_body_lgl = "T",
funding_1L_chr = "'Details on study funders go here.'",
fl_nm_1L_chr = "'Manuscript'",
outp_formats_chr = "'PDF'",
rmd_fl_nms_ls = "make_rmd_fl_nms_ls()",
tables_in_body_lgl = "T",
title_1L_chr = "'Manuscript title goes here.'"
)),
class_desc_chr= "Metadata about a scientific summary manuscript",
parent_class_chr = "Ready4Module")
)
datasets_ls <- list(tibble::tibble(first_nm_chr = c("Alejandra","Fionn"),
middle_nm_chr = c("Rocio", "Seamus"),
last_nm_chr = c("Scienceace", "Researchchamp"),
title_chr = c("Dr", "Prof"),
qualifications_chr = c("MD, PhD", "MSc, PhD"),
institute_chr = c("Insitute_A, Institute_B", "Institute_C, Institute_B"),
sequence_int = c(1,2) %>% as.integer(),
is_corresponding_lgl = c(T, F),
email_chr = c("fake_email@fake_institute.com", "fake_email@made_up_org.com"),
is_equal_first_lgl = c(F,F)) %>%
ready4fun::make_pkg_ds_ls(db_1L_chr = "authors_tb",
desc_1L_chr = "Example of an authors table with fake author entries",
title_1L_chr = "Example authors table",
url_1L_chr = "https://ready4-dev.com"),
tibble::tibble(short_name_chr = c("Insitute_A", "Institute_B", "Institute_C"),
long_name_chr = c("Awesome University, Shanghai","August Institution, London","Highly Ranked Uni, Montreal")) %>%
ready4fun::make_pkg_ds_ls(db_1L_chr = "institutes_tb",
desc_1L_chr = "Example of an institutes table with fake institute entries",
title_1L_chr = "Example institutes table",
url_1L_chr = "https://ready4-dev.com"))
z <- ready4pack::make_pt_ready4pack_manifest(x,
constructor_r3 = y,
pkg_ds_ls_ls = datasets_ls,
clss_to_apply_ls = list(ready4show_authors = c("authors_tb"),
ready4show_institutes = "institutes_tb")) %>%
ready4pack::ready4pack_manifest()
z <- author(z)
#write_extra_pkgs_to_actions(path_to_dir_1L_chr = ".github/workflows")
write_to_edit_workflow("pkgdown.yaml", consent_1L_chr = "Y") # In other packages, run for "test-coverage.yaml" as well.
write_to_tidy_pkg(manifest_ls, build_vignettes_1L_lgl = TRUE,
clean_license_1L_lgl = TRUE, consent_1L_chr = "Y",
examples_chr = character(0), project_1L_chr = "Framework"#, suggest_chr = "pkgload"
)
readLines("README.md") %>% # update in ready4fun
#gsub(pattern = "doi:10.48550/arXiv.([^&]+)", replacement = "https://arxiv.org/abs/\\1") %>%
gsub(pattern = "doi:([^&]+)", replacement = "https://doi.org/\\1") %>%
writeLines(con = "README.md")
#usethis::use_package("pkgload", type = "Suggests") # ??
# write_examples(consent_1L_chr = "Y", path_1L_chr = x$initial_ls$path_to_pkg_rt_1L_chr)
# write_examples(consent_1L_chr = "Y", path_1L_chr = x$initial_ls$path_to_pkg_rt_1L_chr, type_1L_chr = "r4")
# readLines("_pkgdown.yml") %>%
# stringr::str_replace_all(" - text: Model", " - text: Framework") %>%
# writeLines(con = "_pkgdown.yml")
# unlink("LICENSE")
# readLines("DESCRIPTION") %>%
# purrr::map_chr(~.x %>% stringr::str_replace("GPL-3 \\+ file LICENSE","GPL-3")) %>%
# writeLines("DESCRIPTION")
# devtools::document()
# devtools::build_vignettes()
ready4-dev/ready4show documentation built on June 16, 2024, 8:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(ready4)
library(ready4fun)
x <- ready4fun::make_pkg_desc_ls(pkg_title_1L_chr = "Author Health Economic Analysis Programs and Reporting Templates" %>% tools::toTitleCase(),
pkg_desc_1L_chr = "ready4show provides tools for authoring repeatable analyses and to help automate the generation of scientific summaries for modelling studies implemented with the ready4 framework.
For detailed documentation about the framework and how to 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>.
This development version of the ready4show 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("Glen", "Wiesner", #email = "Glen.Wiesner@vu.edu.au",
role = c("aut"), comment = c(ORCID = "0000-0002-0071-130X")),
utils::person("Orygen", role = c("cph", "fnd")),
utils::person("Australian Government Research Training Program", role =c("fnd")),
utils::person("VicHealth",role = c("fnd")),
utils::person("Victoria University", role =c("fnd"))
),
urls_chr = c("https://ready4-dev.github.io/ready4show/",
"https://github.com/ready4-dev/ready4show",
"https://www.ready4-dev.com/")) %>%
ready4fun::make_manifest(addl_pkgs_ls = ready4fun::make_addl_pkgs_ls(#depends_chr = "ready4",
imports_chr = "knitrBootstrap",
suggests_chr = c("bookdown", "officedown","rmarkdown", "rticles")),
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("make_eq_ref","make_rprt_type_ls",
"print_table",
"write_mdl_plt_fl","write_mkdn_from_pkg","write_rprt")),
#dev_pkgs_chr = c("ready4"),
lifecycle_stage_1L_chr = "experimental",
path_to_pkg_logo_1L_chr = "../../../../../Documentation/Images/ready4show-logo/default.png",
piggyback_to_1L_chr = "ready4-dev/ready4",
ready4_type_1L_chr = "authoring",
zenodo_badge_1L_chr = "[](https://doi.org/10.5281/zenodo.5644568)")
y <- ready4class::ready4class_constructor() %>%
dplyr::bind_rows(ready4class::make_pt_ready4class_constructor(make_s3_lgl = TRUE,
name_stub_chr = "authors",
pt_ls = list(list("tibble")),
pt_chkr_pfx_ls = list(list("is_")),
pt_ns_ls = list(list("tibble")),
vals_ls = list(list(first_nm_chr = "character(0)",
middle_nm_chr = "character(0)",
last_nm_chr = "character(0)",
title_chr = "character(0)",
qualifications_chr = "character(0)",
institute_chr = "character(0)",
sequence_int = "integer(0)",
is_corresponding_lgl = "logical(0)",
email_chr = "character(0)",
is_equal_first_lgl = "logical(0)")),
class_desc_chr = "Authors lookup table"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = TRUE,
name_stub_chr = "institutes",
pt_ls = list(list("tibble")),
pt_chkr_pfx_ls = list(list("is_")),
pt_ns_ls = list(list("tibble")),
vals_ls = list(list(short_name_chr = "character(0)",
long_name_chr = "character(0)")),
class_desc_chr = "Institutes lookup table"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = TRUE,
name_stub_chr = "correspondences",
pt_ls = list(list("tibble")),
pt_chkr_pfx_ls = list(list("is_")),
pt_ns_ls = list(list("tibble")),
vals_ls = list(list(old_nms_chr = "character(0)",
new_nms_chr = "character(0)")),
class_desc_chr = "Name correspondences lookup table"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Paths",
slots_ls = list("mkdn_data_dir_1L_chr",
"mkdn_source_dir_1L_chr",
"ms_mkdn_dir_1L_chr",
"ms_dir_1L_chr",
"outp_data_dir_1L_chr",
"reports_dir_1L_chr") %>% list(),
pt_ls = list("character",
"character",
"character",
"character",
"character",
"character") %>% list(),
# vals_ls = list(list(mkdn_data_dir_1L_chr = "'Markdown'",
# ms_mkdn_dir_1L_chr = "'Manuscript'",
# ms_dir_1L_chr = "'Manuscript'",
# outp_data_dir_1L_chr = "'Output'",
# reports_dir_1L_chr = "'Reports'")),
class_desc_chr= "Metadata about paths to Markdown input and output",
parent_class_chr = "Ready4Module"),
ready4class::make_pt_ready4class_constructor(make_s3_lgl = FALSE,
name_stub_chr = "Synopsis",
slots_ls = list("a_Ready4showPaths",
"abstract_args_ls",
"authors_r3",
"background_1L_chr",
"coi_1L_chr",
"conclusion_1L_chr",
"correspondences_r3",
"digits_int",
"ethics_1L_chr",
"fl_nm_1L_chr",
"figures_in_body_lgl",
"funding_1L_chr",
"institutes_r3",
"interval_chr",
"keywords_chr",
"outp_formats_chr",
"rmd_fl_nms_ls",
"sample_desc_1L_chr",
"tables_in_body_lgl",
"title_1L_chr") %>% list(),
pt_ls = list("Ready4showPaths",
"list",
"ready4show_authors",
"character",
"character",
"character",
"ready4show_correspondences",
"integer",
"character",
"character",
"logical",
"character",
"ready4show_institutes",
"character",
"character",
"character",
"list",
"character",
"logical",
"character") %>% list(),
vals_ls = list(list(a_Ready4showPaths = "make_default_paths()",
abstract_args_ls = "make_abstract_args_ls()",
coi_1L_chr = "'None declared.'",
digits_int = "3L",
ethics_1L_chr = "'Details on ethics approvals go here.'",
figures_in_body_lgl = "T",
funding_1L_chr = "'Details on study funders go here.'",
fl_nm_1L_chr = "'Manuscript'",
outp_formats_chr = "'PDF'",
rmd_fl_nms_ls = "make_rmd_fl_nms_ls()",
tables_in_body_lgl = "T",
title_1L_chr = "'Manuscript title goes here.'"
)),
class_desc_chr= "Metadata about a scientific summary manuscript",
parent_class_chr = "Ready4Module")
)
datasets_ls <- list(tibble::tibble(first_nm_chr = c("Alejandra","Fionn"),
middle_nm_chr = c("Rocio", "Seamus"),
last_nm_chr = c("Scienceace", "Researchchamp"),
title_chr = c("Dr", "Prof"),
qualifications_chr = c("MD, PhD", "MSc, PhD"),
institute_chr = c("Insitute_A, Institute_B", "Institute_C, Institute_B"),
sequence_int = c(1,2) %>% as.integer(),
is_corresponding_lgl = c(T, F),
email_chr = c("fake_email@fake_institute.com", "fake_email@made_up_org.com"),
is_equal_first_lgl = c(F,F)) %>%
ready4fun::make_pkg_ds_ls(db_1L_chr = "authors_tb",
desc_1L_chr = "Example of an authors table with fake author entries",
title_1L_chr = "Example authors table",
url_1L_chr = "https://ready4-dev.com"),
tibble::tibble(short_name_chr = c("Insitute_A", "Institute_B", "Institute_C"),
long_name_chr = c("Awesome University, Shanghai","August Institution, London","Highly Ranked Uni, Montreal")) %>%
ready4fun::make_pkg_ds_ls(db_1L_chr = "institutes_tb",
desc_1L_chr = "Example of an institutes table with fake institute entries",
title_1L_chr = "Example institutes table",
url_1L_chr = "https://ready4-dev.com"))
z <- ready4pack::make_pt_ready4pack_manifest(x,
constructor_r3 = y,
pkg_ds_ls_ls = datasets_ls,
clss_to_apply_ls = list(ready4show_authors = c("authors_tb"),
ready4show_institutes = "institutes_tb")) %>%
ready4pack::ready4pack_manifest()
z <- author(z)
#write_extra_pkgs_to_actions(path_to_dir_1L_chr = ".github/workflows")
write_to_edit_workflow("pkgdown.yaml", consent_1L_chr = "Y") # In other packages, run for "test-coverage.yaml" as well.
write_to_tidy_pkg(manifest_ls, build_vignettes_1L_lgl = TRUE,
clean_license_1L_lgl = TRUE, consent_1L_chr = "Y",
examples_chr = character(0), project_1L_chr = "Framework"#, suggest_chr = "pkgload"
)
readLines("README.md") %>% # update in ready4fun
#gsub(pattern = "doi:10.48550/arXiv.([^&]+)", replacement = "https://arxiv.org/abs/\\1") %>%
gsub(pattern = "doi:([^&]+)", replacement = "https://doi.org/\\1") %>%
writeLines(con = "README.md")
#usethis::use_package("pkgload", type = "Suggests") # ??
# write_examples(consent_1L_chr = "Y", path_1L_chr = x$initial_ls$path_to_pkg_rt_1L_chr)
# write_examples(consent_1L_chr = "Y", path_1L_chr = x$initial_ls$path_to_pkg_rt_1L_chr, type_1L_chr = "r4")
# readLines("_pkgdown.yml") %>%
# stringr::str_replace_all(" - text: Model", " - text: Framework") %>%
# writeLines(con = "_pkgdown.yml")
# unlink("LICENSE")
# readLines("DESCRIPTION") %>%
# purrr::map_chr(~.x %>% stringr::str_replace("GPL-3 \\+ file LICENSE","GPL-3")) %>%
# writeLines("DESCRIPTION")
# devtools::document()
# devtools::build_vignettes()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.