In ready4-dev/TTU: Implement Transfer to Utility Mapping Algorithms

This procedure is wrong and should not be implemented. Major edit pending.

knitr::opts_chunk$set(echo = TRUE)
library(magrittr)

here::i_am("Analyses/AQoL-6D/AQol_6D longitudinal/aqol6d_ttu_analysis/Markdown/Child_RMDs/_Make_Raw_Synthetic_Pop.Rmd")

raw_data_tb <- readRDS(here::here("Data cleaning","Data","Combined_cleaned_V4.rds")) %>%
  add_interval_var()
  # dplyr::group_by(fkClientID) %>%
  # dplyr::mutate(bl_date_dtm = d_interview_date %>% dplyr::first()) %>%
  # dplyr::mutate(interval_dbl = purrr::map2_dbl(bl_date_dtm,
  #                                              d_interview_date,
  #                                              ~ lubridate::interval(.x, .y) %>%
  # lubridate::time_length(unit = "days"))) %>%
  # dplyr::ungroup()

intervals_lup_tb <- raw_data_tb %>%
  dplyr::select(fkClientID,d_interview_date, bl_date_dtm, interval_dbl, round) %>%
  dplyr::arrange(fkClientID)

raw_data_tb %>% dplyr::filter(round==1) %>% dplyr::pull(interval_dbl) %>% summary()

raw_data_tb %>% dplyr::filter(round==2) %>% dplyr::pull(interval_dbl) %>% summary()

raw_data_tb <- raw_data_tb %>% 
  dplyr::select(fkClientID, round, interval_dbl,  #d_interview_date,
                c_p_diag_s , s_centre, c_clinical_staging_s, 
                d_age, d_gender, d_sex_birth_s , d_sexual_ori_s,
                d_country_bir_s, d_ATSI,d_english_home, d_english_native, 
                d_relation_s,  d_studying_working, k6_total, 
                phq9_total, bads_total, gad7_total,oasis_total,
                scared_total, participation,
                contains("aqol6d"),c_sofas)
fk_data_ls <- synthpop::syn(raw_data_tb, visit.sequence = names(raw_data_tb)[!names(raw_data_tb) %in% c("fkClientID")], seed = 1234)

fk_data_ls$syn %>% dplyr::filter(round==1) %>% dplyr::pull(interval_dbl) %>% summary()

fk_data_ls$syn %>% dplyr::filter(round==2) %>% dplyr::pull(interval_dbl) %>% summary()

fk_data_tb <- fk_data_ls$syn %>%
  # dplyr::left_join(intervals_lup_tb %>% dplyr::select(fkClientID,bl_date_dtm, round)) %>%
  # dplyr::group_by(fkClientID) %>%
  # dplyr::mutate(bl_date_dtm = sample(intervals_lup_tb$bl_date_dtm, size = 1)) %>%
  # dplyr::ungroup() %>%
  # dplyr::mutate(d_interview_date = purrr::map2(bl_date_dtm,
  #                                              interval_dbl,
  #                                              ~ ifelse(is.na(.y),NA,.x + lubridate::days(.y))) %>% unlist() %>% as.Date(origin = "1970-01-01")) %>%
                  # dplyr::case_when(round = 2 & !(is.na(interval_dbl)|is.na(bl_date_dtm) )~ bl_date_dtm + lubridate::days(interval_dbl),
                  #                                   T ~ bl_date_dtm)
                # ) %>%
 # dplyr::select(-c(bl_date_dtm,interval_dbl)) %>%
    dplyr::arrange(fkClientID)

summary(intervals_lup_tb$bl_date_dtm)

test_tb <- fk_data_tb %>%
    dplyr::ungroup() %>%
  dplyr::arrange(fkClientID) %>%
dplyr::group_by(fkClientID) %>%
  dplyr::arrange(d_interview_date) %>%
  dplyr::mutate(bl_date_dtm2 = d_interview_date %>% dplyr::first()) %>%
  dplyr::mutate(interval_dbl2 = purrr::map2_dbl(bl_date_dtm2,
                                             d_interview_date,
                                             ~ lubridate::interval(.x, .y) %>%
                                               lubridate::time_length(unit = "days"))) %>%
  dplyr::ungroup() 

test_tb %>% dplyr::filter(round==2) %>% dplyr::pull(interval_dbl2) %>% summary()

test_tb %>% dplyr::filter(round==2) %>% dplyr::pull(interval_dbl) %>% summary()

fk_data_tb <- fk_data_tb %>%
  dplyr::select(names(fk_data_tb)[!(names(fk_data_tb) %>% purrr::map_lgl(~ startsWith(.x,"aqol6d_sub") | startsWith(.x,"aqol6d_tot") | startsWith(.x,"aqol6d_fla")))])

reltv_path_1L_chr <-ifelse(params$is_child_1L_lgl,
                           "../../../Output/",
                           "../../Output/"
                           )
saveRDS(fk_data_tb,paste0(reltv_path_1L_chr,"fk_data_tb.rds"))
# tempfile(paste0(here::here("AQol_6D longitudinal/Output"),"/fk_data_tb"), fileext = ".RDS")