scorz: Score Multi-Attribute Utility Instruments

####
# devtools::load_all()
# library(youthvars)
# devtools::load_all()
# x <- ready4use::Ready4useRepos(dv_nm_1L_chr = "fakes",
#                     dv_ds_nm_1L_chr = "https://doi.org/10.7910/DVN/HJXYKQ",
#                     dv_server_1L_chr = "dataverse.harvard.edu")
# objects_ls <- ingest(x,
#                      fls_to_ingest_chr = c("eq5d_ds_tb","eq5d_ds_dict"),
#                      metadata_1L_lgl = F)
# y <- youthvars::YouthvarsSeries(a_Ready4useDyad = x,
#                                 id_var_nm_1L_chr = "fkClientID",
#                                 timepoint_var_nm_1L_chr = "round",
#                                 timepoint_vals_chr = levels(x@ds_tb$round))
# z <- ScorzEuroQol5()
# y@
# maui_params_ls <- make_maui_params_ls(maui_domains_pfxs_1L_chr = "eq5dq_", # NEEDS TO BE SAME ORDER AS SHORT NAMES
#                                       maui_itm_short_nms_chr = c("Mobility", "Self-care", "Activities","Pain","Anxiety"),
#                                       maui_scoring_fn = function(data_tb,
#                                                                  maui_item_pfx_1L_chr,
#                                                                  id_var_nm_1L_chr,
#                                                                  utl_wtd_var_nm_1L_chr,
#                                                                  utl_unwtd_var_nm_1L_chr){
#                                         require(eq5d)
#                                         data_tb %>%
#                                           dplyr::rename_with(~stringr::str_replace(.x,maui_item_pfx_1L_chr,""),
#                                                              dplyr::starts_with(maui_item_pfx_1L_chr)) %>%
#                                           dplyr::mutate(`:=`(!!rlang::sym(utl_wtd_var_nm_1L_chr),
#                                                              eq5d::eq5d(., country="UK", version = "5L", type = "CW"))) %>%
#                                           dplyr::rename_with(~paste0(maui_item_pfx_1L_chr,.x),c("MO","SC","UA","PD","AD")) %>%
#                                           dplyr::mutate(`:=`(!!rlang::sym(utl_unwtd_var_nm_1L_chr),                                          rowSums(dplyr::across(dplyr::starts_with(maui_item_pfx_1L_chr))))) %>%
#                                           dplyr::filter(!is.na(!!rlang::sym(utl_unwtd_var_nm_1L_chr)))
#                                       },
#                                       short_and_long_nm = c("EQ-5D",
#                                                             "EuroQol - Five Dimension"))
# library(scorz)
# a <- ingest(Ready4useRepos(gh_repo_1L_chr = "ready4-dev/scorz",
#                            gh_tag_1L_chr = "Documentation_0.0"),
#             fls_to_ingest_chr = c("aqol_scrg_dict_r3")) %>%
#   procureSlot("b_Ready4useIngest") %>%
#   procure(fl_nm_1L_chr = "aqol_scrg_dict_r3")
#
#
# ScorzProfile <- methods::setClass("ScorzProfile", #scorz
#                                   contains = "Ready4Module",
#                                   slots = c(a_YouthvarsProfile = "YouthvarsProfile",
#                                             domain_unwtd_var_nms_chr = "character",
#                                             domain_wtd_var_nms_chr = "character",
#                                             instrument_dict_r3 = "ready4use_dictionary",
#                                             instrument_nm_1L_chr = "character",
#                                             itm_labels_chr = "character",
#                                             itm_prefix_1L_chr =  "character",
#                                             scrg_dss_ls = "list",
#                                             total_wtd_var_nm_1L_chr = "character",
#                                             total_unwtd_var_nm_1L_chr = "character"),
#                                   prototype = list(a_YouthvarsProfile = YouthvarsProfile(),
#                                                    domain_unwtd_var_nms_chr = NA_character_,
#                                                    domain_wtd_var_nms_chr = NA_character_,
#                                                    instrument_dict_r3 = ready4use::ready4use_dictionary(),
#                                                    instrument_nm_1L_chr = NA_character_,
#                                                    itm_labels_chr = NA_character_,
#                                                    itm_prefix_1L_chr =  NA_character_,
#                                                    scrg_dss_ls = list(),
#                                                    total_wtd_var_nm_1L_chr = NA_character_,
#                                                    total_unwtd_var_nm_1L_chr = NA_character_))
# ScorzAqol6 <- methods::setClass("ScorzAqol6",
#                                 contains = "ScorzProfile",
#                                 slots = c(a_YouthvarsProfile = "YouthvarsProfile",
#                                           domain_unwtd_var_nms_chr = "character",
#                                           domain_wtd_var_nms_chr = "character",
#                                           instrument_dict_r3 = "ready4use_dictionary",
#                                           instrument_nm_1L_chr = "character",
#                                           itm_labels_chr = "character",
#                                           itm_prefix_1L_chr =  "character",
#                                           scrg_dss_ls = "list",
#                                           total_wtd_var_nm_1L_chr = "character",
#                                           total_unwtd_var_nm_1L_chr = "character"),
#                                 prototype = list(a_YouthvarsProfile = YouthvarsProfile(),
#                                                  domain_unwtd_var_nms_chr = NA_character_,
#                                                  domain_wtd_var_nms_chr = paste0("vD",1:6),
#                                                  instrument_dict_r3 = youthvars::aqol_scrg_dict_r3,
#                                                  instrument_nm_1L_chr = "Assessment of Quality of Life (6 Dimension)",
#                                                  itm_labels_chr = c("Household tasks", "Getting around",
#                                                                     "Morbility","Self care","Enjoy close rel\'s",
#                                                                     "Family rel\'s", "Community involv\'t",
#                                                                     "Despair","Worry", "Sad", "Agitated",
#                                                                     "Energy level", "Control", "Coping",
#                                                                     "Frequency of pain", "Degree of pain",
#                                                                     "Pain interference","Vision", "Hearing",
#                                                                     "Communication"),
#                                                  itm_prefix_1L_chr =  "aqol6d_q",
#                                                  scrg_dss_ls = list(),
#                                                  total_wtd_var_nm_1L_chr = "aqol6d_total_w",
#                                                  total_unwtd_var_nm_1L_chr = "aqol6d_total_c"))
# ScorzAqol6Adol <- methods::setClass("ScorzAqol6Adol",
#                                     contains = "ScorzAqol6",
#                                     prototype = list(instrument_nm_1L_chr = "Assessment of Quality of Life (6 Dimension, Adolescent Version)"))
#

# methods::setMethod("depict",
#                    methods::className("ScorzProfile"#, package = "ready4use"
#                    ),
#                    depict_ScorzProfile)
#
# methods::setMethod("renew",
#                    methods::className("ScorzAqol6Adol"#, package = "ready4use"
#                    ),
#                    renew_ScorzAqol6Adol)
###
# x <- ready4use::Ready4useRepos(dv_nm_1L_chr = "fakes",
#                                dv_ds_nm_1L_chr = "https://doi.org/10.7910/DVN/W95KED",
#                                dv_server_1L_chr = "dataverse.harvard.edu") %>%
#   ingest(fls_to_ingest_chr = "ymh_clinical_dyad_r4") # MAKE DEFAULT PROCURE METHOD IF RETURN FILE ==T
# x <- procure(procureSlot(x,"b_Ready4useIngest"), # MAKE DEFAULT PROCURE METHOD FOR RECORD IF FL NM PROVIDED
#              fl_nm_1L_chr = "ymh_clinical_dyad_r4")
# exhibit(x)
# y <- youthvars::YouthvarsSeries(a_Ready4useDyad = x,
#                                 id_var_nm_1L_chr = "fkClientID",
#                                 timepoint_var_nm_1L_chr = "round",
#                                 timepoint_vals_chr = levels(x@ds_tb$round))
# z <- ScorzAqol6Adol(a_YouthvarsProfile = y)#,itm_prefix_1L_chr = "aqol6d_q"
# z <- renew(z)
# x <- procureSlot(procureSlot(z,"a_YouthvarsProfile"),
#                  "a_Ready4useDyad")
# exhibit(x)
#
# depict(z, type_1L_chr = "domain_by_time")
# depict(z, type_1L_chr = "domain_by_time", var_idcs_int = c(1L))
# #depict(z, type_1L_chr = "item_by_time")
# depict(z, type_1L_chr = "item_by_time", var_idcs_int = c(2L))
# depict(z, type_1L_chr = "total_by_time")
# depict(z, type_1L_chr = "comp_item_by_time")
# depict(z, type_1L_chr = "comp_domain_by_time")
##
## MIGRATE TO SPECIFIC
# ScorzModelSpec <- methods::setClass("ScorzModelSpec", #youthvars
#                                     contains = "Ready4Module",
#                                     slots = c(a_ScorzProfile = "ScorzProfile",
#                                               candidate_predrs_chr = "character",
#                                               depnt_var_nm_1L_chr = "character",
#                                               depnt_var_max_val_1L_dbl = "numeric"),
#                                     prototype =  list(a_ScorzProfile = ScorzProfile(),
#                                                       candidate_predrs_chr = NA_character_,
#                                                       depnt_var_nm_1L_chr = NA_character_,
#                                                       depnt_var_max_val_1L_dbl = Inf))
# exhibit_ScorzModelSpec <- function(x,
#                                    captions_chr = character(0),
#                                    method_chr = c("pearson", "spearman"),
#                                    mkdn_tbl_refs_chr = NULL,
#                                    output_type_1L_chr = "HTML",
#                                    type_1L_chr = "correlation",
#                                    timepoints_int = NA_integer_){
#   if(type_1L_chr == "correlation"){
#     if(is.na(timepoints_int)){
#       if("timepoint_vals_chr" %in% slotNames(x@a_ScorzProfile@a_YouthvarsProfile)){
#         timepoints_int <- 1:length(x@a_ScorzProfile@a_YouthvarsProfile@timepoint_vals_chr) %>% as.integer()
#       }else{
#         timepoints_int <- 1
#       }
#     }
#     if(identical(character(0), captions_chr)){
#       captions_chr <- paste0("Correlations at ",
#                              x@a_ScorzProfile@a_YouthvarsProfile@timepoint_vals_chr[timepoints_int])
#     }
#     1:length(timepoints_int) %>%
#       purrr::map(~
#                    transform_ds_for_tstng(x@a_ScorzProfile@a_YouthvarsProfile@a_Ready4useDyad@ds_tb,
#                                           depnt_var_nm_1L_chr = x@depnt_var_nm_1L_chr,
#                                           depnt_var_max_val_1L_dbl = x@depnt_var_max_val_1L_dbl,
#                                           candidate_predrs_chr = x@candidate_predrs_chr,
#                                           round_var_nm_1L_chr = ifelse("timepoint_var_nm_1L_chr" %in% slotNames(x@a_ScorzProfile@a_YouthvarsProfile),
#                                                                        x@a_ScorzProfile@a_YouthvarsProfile@timepoint_var_nm_1L_chr,
#                                                                        NA_character_),
#                                           round_val_1L_chr = ifelse("timepoint_vals_chr" %in% slotNames(x@a_ScorzProfile@a_YouthvarsProfile),
#                                                                     x@a_ScorzProfile@a_YouthvarsProfile@timepoint_vals_chr[timepoints_int[.x]],
#                                                                     NA_character_))  %>%
#                    make_corstars_tbl_xx(caption_1L_chr = captions_chr[.x],
#                                         mkdn_tbl_ref_1L_chr = mkdn_tbl_refs_chr[.x],
#                                         method_chr = method_chr,
#                                         result_chr = output_type_1L_chr
#                    ))
#   }
# }
# methods::setMethod("exhibit",
#                    methods::className("ScorzModelSpec"#, package = "ready4use"
#                    ),
#                    exhibit_ScorzModelSpec)

#