Nothing
R/elixhauser.R
In multimorbidity: Harmonizing Various Comorbidity, Multimorbidity, and Frailty Measures
Defines functions
elixhauser
Documented in
elixhauser
#' Elixhauser Comorbidities
#'
#' \code{elixhauser} returns a summary dataset containing the Elixhauser comorbidities for
#' each patient.
#'
#' This function uses data which has been properly prepared to identify and flag the
#' Elixhauser comorbidities. See full package documentation for additional details.
#'
#' @param dat dataset which has been properly prepared using 'prepare_data()'
#' @param id variable of the unique patient identifier
#' @param dx the column with the diagnoses (defaults to 'dx')
#' @param version which version(s) of ICD your data contain (ICD-9 only: 9, ICD-10 only: 10,
#' Both: 19)
#' @param version_var variable which denotes if the diagnoses on that row are ICD-9 (9) or
#' ICD-10 (10)
#' @param outpatient_two whether or not it should be required for there to be two outpatient
#' claims for a diagnosis for a patient to be positively coded with that diagnosis.
#'
#' @return dataframe with one row per patient, and a column for their patient id, a column with each
#' Elixhauser comorbidity, and a column with their Elixhauser index for readmission and death
#'
#' @examples
#' elixhauser(dat = prepared_data, id = patient_id, dx = dx, version = 19,
#' version_var = version, outpatient_two = "yes")
#'
#'
#' @export
#' @importFrom rlang .data
elixhauser <- function(dat = NULL,
id = NULL,
dx = "dx",
version = 19,
version_var = NULL,
outpatient_two = "no"){
id2 <- rlang::quo_name(rlang::enquo(id))
# Elixhauser ICD-9 ----
## Diagnoses Setup ----
if (version == 9){
chf9 <- c("39891", "40201", "40211", "40291", "40401", "40403", "40411", "40413", "40491", "40493",
"4254", "4255", "4257", "4258", "4259")
valve9 <- c("3979", "V422", "V433", "7463", "7464", "7465", "7466")
pulmcirc9 <- c("4179")
periph_vasc9 <- c("44421", "44422", "4471", "449", "4471", "5571", "5579", "V434")
paralysis9 <- c("3449", "78072")
neuro9 <- c("3334", "3335", "33385", "33394", "3452", "3453", "78097", "7843")
chronic_pulm9 <- c("5064")
diab_c9 <- c("7751")
hypo9 <- c("243", "2440", "2441", "2442", "2448", "2449")
renal9 <- c("5853", "5854 ", "5855 ", "5856 ", "5859 ", "586", "V420", "V451", "V4511", "V4512")
liver9 <- c("07022", "07023", "07032", "07033", "07044", "07054", "4560",
"4561", "45620", "45621", "5710", "5712 ", "5713", "5715", "5716",
"5718", "5719", "5723", "5728", "5735", "V427")
peptic9 <- c("53141", "53151", "53161", "53170", "53171", "53191", "53241",
"53251", "53261", "53270", "53271", "53291", "53341", "53351",
"53361", "53370", "53371", "53391", "53441", "53451", "53461",
"53470", "53471", "53491")
mets9 <- c("1990", "1991", "78951")
rheum9 <- c("7010")
coag9 <- c("2871", "28984")
obese9 <- c("2780", "V8554", "79391")
weightloss9 <- c("78321", "78322")
bld_anem9 <- c("2800")
alc9 <- c("2910", "2911", "2912", "2913", "2915", "2919")
drug9 <- c("2920", "2929")
depress9 <- c("3004", "30112", "3090", "3091","311")
chf9_str <- ("428")
valve9_str <- c("424", "0932", "394", "395", "396", "397")
pulmcirc9_str <- c("4151", "416")
periph_vasc9_str <- c("440", "441", "442", "4431", "4432", "4438", "4439")
htn_uc9_str <- c("4011", "4019", "6420")
htn_c9_str <- c("402", "403", "404", "405", "6422", "6421", "6427", "6429")
paralysis9_str <- c("342", "343", "3440", "3441", "3442", "3443", "3444", "3445", "3446", "4382", "4383", "4384", "4385")
neuro9_str <- c("330", "331", "332", "3337", "3334", "3335", "3338", "340", "341","3450", "3451", "3454", "3455", "3456",
"3457", "3458", "3459", "347", "6494", "7687", "7803")
chronic_pulm9_str <- c("490", "491", "492", "493", "494", "495", "496", "500", "501", "502")
diab_uc9_str <- c("2500", "2501", "2502", "2503", "6480", "2490", "2491", "2492", "2493")
diab_c9_str <- c("2504", "2505", "2506", "2507", "2508", "2509", "2494", "2495", "2496", "2497", "2498", "2499")
renal9_str <- c("V560", "V561", "V562", "V563", "V568")
liver9_str <- c("5714")
hiv9_str <- c("042", "043", "044")
lymph9_str <- c("200", "201", "2020", "2021", "2022", "2025", "2026", "2027", "2028", "2029", "203", "2386", "2733")
mets9_str <- c("196", "197", "198", "209")
tumor9_str <- c("14, 15, 16, 170", "171", "172", "174", "175", "179",
"18", "190", "191", "192", "193", "194", "195", "2090", "2091", "2092", "2093", "2580")
rheum9_str <- c("710", "714", "720", "725")
coag9_str <- c("286", "2873", "2874", "2875", "6493")
obese9_str <- c("2780", "6491", "V853", "V854")
weightloss9_str <- c("260", "261", "262", "263")
fluid9_str <- c("276")
bld_anem9_str <- c("6482")
def_anem9_str <- c("280", "2852", "2859")
alcohol9_str <- c("2918", "303", "3050")
drug9_str <- c("2928", "304", "3052", "3053", "3054", "3055", "3056", "3057", "3058", "3059", "6483")
psych9_str <- c("295", "296", "297", "298", "2991")
## Code ----
dat1 <- dat %>%
dplyr::mutate(chf = dplyr::if_else(dx %in% chf9 | stringr::str_starts(dx, paste(chf9_str)), 1, 0),
valve = dplyr::if_else(dx %in% valve9 | stringr::str_starts(dx, paste(valve9_str, sep = "|", collapse = "|")), 1, 0),
pulmcirc = dplyr::if_else(dx %in% pulmcirc9 | stringr::str_starts(dx, paste(pulmcirc9_str, sep = "|", collapse = "|")), 1, 0),
periph_vasc = dplyr::if_else(dx %in% periph_vasc9 | stringr::str_starts(dx, paste(periph_vasc9_str, sep = "|", collapse = "|")), 1, 0),
htn_uc = dplyr::if_else(stringr::str_starts(dx, paste(htn_uc9_str, sep = "|", collapse = "|")), 1, 0),
htn_c = dplyr::if_else(stringr::str_starts(dx, paste(htn_c9_str, sep = "|", collapse = "|")), 1 ,0),
paralysis = dplyr::if_else(dx %in% paralysis9 | stringr::str_starts(dx, paste(paralysis9_str, sep = "|", collapse = "|")), 1, 0),
neuro = dplyr::if_else(dx %in% neuro9 | stringr::str_starts(dx, paste(neuro9_str, sep = "|", collapse = "|")), 1, 0),
chronic_pulm = dplyr::if_else(dx %in% chronic_pulm9 | stringr::str_starts(dx, paste(chronic_pulm9_str, sep = "|", collapse = "|")), 1, 0),
diab_uc = dplyr::if_else(stringr::str_starts(dx, paste(diab_uc9_str, sep = "|", collapse = "|")), 1, 0),
diab_c = dplyr::if_else(dx %in% diab_c9 | stringr::str_starts(dx, paste(diab_c9_str, sep = "|", collapse = "|")), 1, 0),
hypo = dplyr::if_else(dx %in% hypo9, 1, 0),
renal = dplyr::if_else(dx %in% renal9 | stringr::str_starts(dx, paste(renal9_str, sep = "|", collapse = "|")), 1, 0),
liver = dplyr::if_else(dx %in% liver9 | stringr::str_starts(dx, paste(liver9_str)), 1, 0),
peptic = dplyr::if_else(dx %in% peptic9, 1, 0),
hiv = dplyr::if_else(stringr::str_starts(dx, paste(hiv9_str, sep = "|", collapse = "|")), 1 ,0),
lymph = dplyr::if_else(stringr::str_starts(dx, paste(lymph9_str, sep = "|", collapse = "|")), 1, 0),
mets = dplyr::if_else(dx %in% mets9 | stringr::str_starts(dx, paste(mets9_str, sep = "|", collapse = "|")), 1, 0),
tumor = dplyr::if_else(stringr::str_starts(dx, paste(tumor9_str, sep = "|", collapse = "|")), 1, 0),
rheum = dplyr::if_else(dx %in% rheum9 | stringr::str_starts(dx, paste(rheum9_str, sep = "|", collapse = "|")), 1, 0),
coag = dplyr::if_else(dx %in% coag9 | stringr::str_starts(dx, paste(coag9_str, sep = "|", collapse = "|")), 1, 0),
obese = dplyr::if_else(dx %in% obese9 | stringr::str_starts(dx, paste(obese9_str, sep = "|", collapse = "|")), 1, 0),
weightloss = dplyr::if_else(dx %in% weightloss9 | stringr::str_starts(dx, paste(weightloss9_str, sep = "|", collapse = "|")), 1, 0),
fluid = dplyr::if_else(stringr::str_starts(dx, paste(fluid9_str)), 1, 0),
bld_anem = dplyr::if_else(dx %in% bld_anem9 | stringr::str_starts(dx, paste(bld_anem9_str)), 1, 0),
def_anem = dplyr::if_else(stringr::str_starts(dx, paste(def_anem9_str, sep = "|", collapse = "|")), 1, 0),
alcohol = dplyr::if_else(dx %in% alc9 | stringr::str_starts(dx, paste(alcohol9_str, sep = "|", collapse = "|")), 1, 0),
drug = dplyr::if_else(dx %in% drug9 | stringr::str_starts(dx, paste(drug9_str, sep = "|", collapse = "|")), 1, 0),
psych = dplyr::if_else(stringr::str_starts(dx, paste(psych9_str, sep = "|", collapse = "|")), 1, 0),
depression = dplyr::if_else(dx %in% depress9, 1, 0))
dat1 <- dat1 %>%
dplyr::mutate(htn_uc = dplyr::if_else(.data$htn_c == 1, 0, .data$htn_uc),
tumor = dplyr::if_else(.data$mets == 1, 0, .data$tumor),
diab_uc = dplyr::if_else(.data$diab_c == 1, 0, .data$diab_uc),
htn_comb = dplyr::if_else(.data$htn_c == 1 | .data$htn_uc == 1, 1, 0)) }
# Elixhauser ICD-10 ----
else if (version == 10){
## Diagnoses Setup ----
hiv10 <- c("B20", "O98711", "O98712", "O98713", "O98719", "O9872", "O9873",
"Z21")
alcohol10 <- c("F1010", "F1011", "F10120", "F10121", "F10129", "F10130",
"F10131", "F10132", "F10139", "F1014", "F10150", "F10151",
"F10159", "F10180", "F10181", "F10182", "F10188", "F1019",
"F1020", "F1021", "F10220", "F10221", "F10229", "F10230",
"F10231", "F10232", "F10239", "F1024", "F10250", "F10251",
"F10259", "F1026", "F1027", "F10280", "F10281", "F10282",
"F10288", "F1029","F1094","F10950","F10951","F10959", "F1096",
"F1097", "F10980", "G621", "I426", "K2920", "K2921", "O99310",
"O99311", "O99312", "O99313", "O99314", "O99315")
alcohol_liver_mild10 <- c("K7010", "K7011")
def_anem10 <- c("D501", "D508", "D509", "D510", "D511", "D512", "D513", "D518",
"D519", "D520", "D521", "D528", "D529", "D530", "D531", "D532",
"D538", "D539", "D630", "D631", "D638", "D649", "O99011",
"O99012", "O99013", "O99019")
rheum10 <- c("A1801", "A1802", "A3984", "A5441","A5442","L4050","L4051","L4054",
"L4059","L900","L940","L941","L943","M01X0","M01X11", "M01X12",
"M01X19","M01X21", "M01X22", "M01X29", "M01X31", "M01X32", "M01X39",
"M01X41","M01X42","M01X49","M01X51","M01X52","M01X59","M01X61","M01X62",
"M01X69","M01X71","M01X72","M01X79","M01X8","M01X9","M0200","M02011",
"M02012","M02019","M02021","M02022","M02029","M02031","M02032","M02039",
"M02041","M02042","M02049","M02051","M02052","M02059","M02061","M02062",
"M02069","M02071","M02072","M02079","M0208","M0209","M0210","M02111",
"M02112","M02119","M02121","M02122","M02129","M02131","M02132","M02139",
"M02141","M02142","M02149","M02151","M02152","M02159","M02161","M02162",
"M02169","M02171","M02172","M02179","M0218","M0219","M0220","M02211",
"M02212","M02219","M02221","M02222","M02229","M02231","M02232","M02239",
"M02241","M02242","M02249","M02251","M02252","M02259","M02261","M02262",
"M02269","M02271","M02272","M02279","M0228","M0229","M0230","M02311",
"M02312","M02319","M02321","M02322","M02329","M02331","M02332","M02339",
"M02341","M02342","M02349","M02351","M02352","M02359","M02361","M02362",
"M02369","M02371","M02372","M02379","M0238","M0239","M0280","M02811",
"M02812","M02819","M02821","M02822","M02829","M02831","M02832","M02839",
"M02841","M02842","M02849","M02851","M02852","M02859","M02861","M02862",
"M02869","M02871","M02872","M02879","M0288","M0289","M029","M0500","M05011",
"M05012","M05019","M05021","M05022","M05029","M05031","M05032","M05039",
"M05041","M05042","M05049","M05051","M05052","M05059","M05061","M05062",
"M05069","M05071","M05072","M05079","M0509","M0510","M05111","M05112",
"M05119","M05121","M05122","M05129","M05131","M05132","M05139","M05141","
M05142","M05149","M05151","M05152","M05159","M05161","M05162","M05169",
"M05171","M05172","M05179","M0519","M0520","M05211","M05212","M05219",
"M05221","M05222","M05229","M05231","M05232","M05239","M05241","M05242",
"M05249","M05251","M05252","M05259","M05261","M05262","M05269","M05271",
"M05272","M05279","M0529","M0530","M05311","M05312","M05319","M05321",
"M05322","M05329","M05331","M05332","M05339","M05341","M05342","M05349",
"M05351","M05352","M05359","M05361","M05362","M05369","M05371","M05372",
"M05379","M0539","M0540","M05411","M05412","M05419","M05421","M05422",
"M05429","M05431","M05432","M05439","M05441","M05442","M05449","M05451",
"M05452","M05459","M05461","M05462","M05469","M05471","M05472","M05479",
"M0549","M0550","M05511","M05512","M05519","M05521","M05522","M05529",
"M05531","M05532","M05539","M05541","M05542","M05549","M05551","M05552",
"M05559","M05561","M05562","M05569","M05571","M05572","M05579","M0559",
"M0560","M05611","M05612","M05619","M05621","M05622","M05629","M05631",
"M05632","M05639","M05641","M05642","M05649","M05651","M05652","M05659",
"M05661","M05662","M05669","M05671","M05672","M05679","M0569","M0570",
"M05711","M05712","M05719","M05721","M05722","M05729","M05731","M05732",
"M05739","M05741","M05742","M05749","M05751","M05752","M05759","M05761",
"M05762","M05769","M05771","M05772","M05779","M0579","M057A","M0580",
"M05811","M05812","M05819","M05821","M05822","M05829","M05831","M05832",
"M05839","M05841","M05842","M05849","M05851","M05852","M05859","M05861",
"M05862","M05869","M05871","M05872","M05879","M0589","M058A","M059",
"M0600","M06011","M06012","M06019","M06021","M06022","M06029","M06031",
"M06032","M06039","M06041","M06042","M06049","M06051","M06052","M06059",
"M06061","M06062","M06069","M06071","M06072","M06079","M0608","M0609",
"M060A","M061","M0620","M06211","M06212","M06219","M06221","M06222",
"M06229","M06231","M06232","M06239","M06241","M06242","M06249","M06251",
"M06252","M06259","M06261","M06262","M06269","M06271","M06272","M06279",
"M0628","M0629","M0630","M06311","M06312","M06319","M06321","M06322",
"M06329","M06331","M06332","M06339","M06341","M06342","M06349","M06351",
"M06352","M06359","M06361","M06362","M06369","M06371","M06372","M06379",
"M0638","M0639","M064","M0680","M06811","M06812","M06819","M06821",
"M06822","M06829","M06831","M06832","M06839","M06841","M06842","M06849",
"M06851","M06852","M06859","M06861","M06862","M06869","M06871","M06872",
"M06879","M0688","M0689","M068A","M069","M0760","M07611","M07612",
"M07619","M07621","M07622","M07629","M07631","M07632","M07639",
"M07641","M07642","M07649","M07651","M07652","M07659","M07661",
"M07662","M07669","M07671","M07672","M07679","M0768","M0769","M0800",
"M08011","M08012","M08019","M08021","M08022","M08029","M08031","M08032",
"M08039","M08041","M08042","M08049","M08051","M08052","M08059","M08061",
"M08062","M08069","M08071","M08072","M08079","M0808","M0809","M080A","M081",
"M0820","M08211","M08212","M08219","M08221","M08222","M08229","M08231",
"M08232","M08239","M08241","M08242","M08249","M08251","M08252","M08259",
"M08261","M08262","M08269","M08271","M08272","M08279","M0828","M0829",
"M082A","M083","M0840","M08411","M08412","M08419","M08421","M08422",
"M08429","M08431","M08432","M08439","M08441","M08442","M08449","M08451",
"M08452","M08459","M08461","M08462","M08469","M08471","M08472","M08479",
"M0848","M084A","M0880","M08811","M08812","M08819","M08821","M08822",
"M08829","M08831","M08832","M08839","M08841","M08842","M08849","M08851",
"M08852","M08859","M08861","M08862","M08869","M08871","M08872","M08879",
"M0888","M0889","M0890","M08911","M08912","M08919","M08921","M08922",
"M08929","M08931","M08932","M08939","M08941","M08942","M08949","M08951",
"M08952","M08959","M08961","M08962","M08969","M08971","M08972","M08979",
"M0898","M0899","M089A","M1200","M12011","M12012","M12019","M12021","M12022",
"M12029","M12031","M12032","M12039","M12041","M12042","M12049","M12051",
"M12052","M12059","M12061","M12062","M12069","M12071","M12072","M12079",
"M1208","M1209","M300","M301","M302","M303","M308","M310","M311","M312",
"M3130","M3131","M314","M315","M316","M317","M318","M319","M320","M3210",
"M3212","M3213","M3214","M3215","M3219","M328","M329","M3300","M3301","M3302",
"M3303","M3309","M3310","M3311","M3312","M3313","M3319","M3320","M3321","M3322",
"M3329","M3390","M3391","M3392","M3393","M3399","M340","M341","M342",
"M3481","M3482","M3483","M3489","M349","M3500","M3501","M3502",
"M3503","M3504","M3509","M351","M352","M353","M355","M356","M358",
"M359","M360","M361","M368","M450","M451","M452","M453","M454",
"M455","M456","M457","M458","M459","M4600","M4601","M4602","M4603",
"M4604","M4605","M4606","M4607","M4608","M4609","M461","M4650",
"M4651","M4652","M4653","M4654","M4655","M4656","M4657","M4658",
"M4659","M4680","M4681","M4682","M4683","M4684","M4685","M4686",
"M4687","M4688","M4689","M4690","M4691","M4692","M4693","M4694",
"M4695","M4696","M4697","M4698","M4699","M4980","M4981","M4982",
"M4983","M4984","M4985","M4986","M4987","M4988","M4989")
bld_loss10 <- c("D500", "O9081", "O9902", "O9903")
leuk10 <- c("C9010","C9011","C9012","C9100","C9101","C9102","C9110","C9111",
"C9112","C9130","C9131","C9132","C9140","C9141","C9142","C9150",
"C9151","C9152","C9160","C9161","C9162","C9190","C9191","C9192",
"C91A0","C91A1","C91A2","C91Z0","C91Z1","C91Z2","C9200","C9201",
"C9202","C9210","C9211","C9212","C9220","C9221","C9222","C9230",
"C9231","C9232","C9240","C9241","C9242","C9250","C9251","C9252",
"C9260","C9261","C9262","C9290","C9291","C9292","C92A0","C92A1",
"C92A2","C92Z0","C92Z1","C92Z2","C9300","C9301","C9302","C9310",
"C9311","C9312","C9330","C9331","C9332","C9390","C9391","C9392",
"C93Z0","C93Z1","C93Z2","C9400","C9401","C9402","C9420","C9421",
"C9422","C9430","C9431","C9432","C9440","C9441","C9442","C946",
"C9480","C9481","C9482","C9500","C9501","C9502","C9510","C9511",
"C9512","C9590","C9591","C9592")
lymph10 <- c("C8100","C8101","C8102","C8103","C8104","C8105","C8106","C8107",
"C8108","C8109","C8110","C8111","C8112","C8113","C8114","C8115",
"C8116","C8117","C8118","C8119","C8120","C8121","C8122","C8123",
"C8124","C8125","C8126","C8127","C8128","C8129","C8130","C8131",
"C8132","C8133","C8134","C8135","C8136","C8137","C8138","C8139",
"C8140","C8141","C8142","C8143","C8144","C8145","C8146","C8147",
"C8148","C8149","C8170","C8171","C8172","C8173","C8174","C8175",
"C8176","C8177","C8178","C8179","C8190","C8191","C8192","C8193",
"C8194","C8195","C8196","C8197","C8198","C8199","C8200","C8201",
"C8202","C8203","C8204","C8205","C8206","C8207","C8208","C8209",
"C8210","C8211","C8212","C8213","C8214","C8215","C8216","C8217",
"C8218","C8219","C8220","C8221","C8222","C8223","C8224","C8225",
"C8226","C8227","C8228","C8229","C8230","C8231","C8232","C8233",
"C8234","C8235","C8236","C8237","C8238","C8239","C8240","C8241",
"C8242","C8243","C8244","C8245","C8246","C8247","C8248","C8249",
"C8250","C8251","C8252","C8253","C8254","C8255","C8256","C8257",
"C8258","C8259","C8260","C8261","C8262","C8263","C8264","C8265",
"C8266","C8267","C8268","C8269","C8280","C8281","C8282","C8283",
"C8284","C8285","C8286","C8287","C8288","C8289","C8290","C8291",
"C8292","C8293","C8294","C8295","C8296","C8297","C8298","C8299",
"C8300","C8301","C8302","C8303","C8304","C8305","C8306","C8307",
"C8308","C8309","C8310","C8311","C8312","C8313","C8314","C8315",
"C8316","C8317","C8318","C8319","C8330","C8331","C8332","C8333",
"C8334","C8335","C8336","C8337","C8338","C8339","C8350","C8351",
"C8352","C8353","C8354","C8355","C8356","C8357","C8358","C8359",
"C8370","C8371","C8372","C8373","C8374","C8375","C8376","C8377",
"C8378","C8379","C8380","C8381","C8382","C8383","C8384","C8385",
"C8386","C8387","C8388","C8389","C8390","C8391","C8392","C8393",
"C8394","C8395","C8396","C8397","C8398","C8399","C8400","C8401",
"C8402","C8403","C8404","C8405","C8406","C8407","C8408","C8409",
"C8410","C8411","C8412","C8413","C8414","C8415","C8416","C8417",
"C8418","C8419","C8440","C8441","C8442","C8443","C8444","C8445",
"C8446","C8447","C8448","C8449","C8460","C8461","C8462","C8463",
"C8464","C8465","C8466","C8467","C8468","C8469","C8470","C8471",
"C8472","C8473","C8474","C8475","C8476","C8477","C8478","C8479",
"C8490","C8491","C8492","C8493","C8494","C8495","C8496","C8497",
"C8498","C8499","C84A0","C84A1","C84A2","C84A3","C84A4","C84A5",
"C84A6","C84A7","C84A8","C84A9","C84Z0","C84Z1","C84Z2","C84Z3",
"C84Z4","C84Z5","C84Z6","C84Z7","C84Z8","C84Z9","C8510","C8511",
"C8512","C8513","C8514","C8515","C8516","C8517","C8518","C8519",
"C8520","C8521","C8522","C8523","C8524","C8525","C8526","C8527",
"C8528","C8529","C8580","C8581","C8582","C8583","C8584","C8585",
"C8586","C8587","C8588","C8589","C8590","C8591","C8592","C8593",
"C8594","C8595","C8596","C8597","C8598","C8599","C860","C861",
"C862","C863","C864","C865","C866","C880","C882","C883","C884",
"C888","C889","C9000","C9001","C9002","C9020","C9021","C9022",
"C9030","C9031","C9032","C960","C962","C9620","C9621","C9622",
"C9629","C964","C969","C96A","C96Z","D47Z9")
mets10 <- c("C770","C771","C772","C773","C774","C775","C778","C779","C7800",
"C7801","C7802","C781","C782","C7830","C7839","C784","C785","C786",
"C787","C7880","C7889","C7900","C7901","C7902","C7910","C7911",
"C7919","C792","C7931","C7932","C7940","C7949","C7951","C7952",
"C7960","C7961","C7962","C7970","C7971","C7972","C7981","C7982",
"C7989","C799","C7B00","C7B01","C7B02","C7B03","C7B04","C7B09",
"C7B1","C7B8","C800")
insitu10 <- c("D0000","D0001","D0002","D0003","D0004","D0005","D0006","D0007",
"D0008","D001","D002","D010","D011","D012","D013","D0140","D0149",
"D015","D017","D019","D020","D021","D0220","D0221","D0222","D023",
"D024","D030","D0310","D0311","D03111","D03112","D0312","D03121",
"D03122","D0320","D0321","D0322","D0330","D0339","D034","D0351",
"D0352","D0359","D0360","D0361","D0362","D0370","D0371","D0372",
"D038","D039","D040","D0410","D0411","D04111","D04112","D0412",
"D04121","D04122","D0420","D0421","D0422","D0430","D0439","D044",
"D045","D0460","D0461","D0462","D0470","D0471","D0472","D048",
"D049","D0500","D0501","D0502","D0510","D0511","D0512","D0580",
"D0581","D0582","D0590","D0591","D0592","D060","D061","D067",
"D069","D070","D071","D072","D0730","D0739","D074","D075",
"D0760","D0761","D0769","D090","D0910","D0919","D0920","D0921",
"D0922","D093","D098","D099")
solid10 <- c("C000","C001","C002","C003","C004","C005","C006","C008","C009",
"C01","C020","C021","C022","C023","C024","C028","C029","C030",
"C031","C039","C040","C041","C048","C049","C050","C051","C052",
"C058","C059","C060","C061","C062","C0680","C0689","C069","C07",
"C080","C081","C089","C090","C091","C098","C099","C100","C101",
"C102","C103","C104","C108","C109","C110","C111","C112","C113",
"C118","C119","C12","C130","C131","C132","C138","C139","C140",
"C142","C148","C153","C154","C155","C158","C159","C160","C161",
"C162","C163","C164","C165","C166","C168","C169","C170","C171",
"C172","C173","C178","C179","C180","C181","C182","C183","C184",
"C185","C186","C187","C188","C189","C19","C20","C210","C211",
"C212","C218","C220","C221","C222","C223","C224","C227","C228",
"C229","C23","C240","C241","C248","C249","C250","C251","C252",
"C253","C254","C257","C258","C259","C260","C261","C269","C300",
"C301","C310","C311","C312","C313","C318","C319","C320","C321",
"C322","C323","C328","C329","C33","C3400","C3401","C3402","C3410",
"C3411","C3412","C342","C3430","C3431","C3432","C3480","C3481",
"C3482","C3490","C3491","C3492","C37","C380","C381","C382","C383",
"C384","C388","C390","C399","C4000","C4001","C4002","C4010","C4011",
"C4012","C4020","C4021","C4022","C4030","C4031","C4032","C4080",
"C4081","C4082","C4090","C4091","C4092","C410","C411","C412",
"C413","C414","C419","C430","C4310","C4311","C43111","C43112",
"C4312","C43121","C43122","C4320","C4321","C4322","C4330",
"C4331","C4339","C434","C4351","C4352","C4359","C4360","C4361",
"C4362","C4370","C4371","C4372","C438","C439","C4400","C4409",
"C44101","C44102","C441021","C441022","C44109","C441091",
"C441092","C44131","C441321","C441322","C441391","C441392",
"C44191","C44192","C441921","C441922","C44199","C441991",
"C441992","C44201","C44202","C44209","C44291","C44292","C44299",
"C44300","C44301","C44309","C44390","C44391","C44399","C4440",
"C4449","C44500","C44501","C44509","C44590","C44591","C44599",
"C44601","C44602","C44609","C44691","C44692","C44699","C44701",
"C44702","C44709","C44791","C44792","C44799","C4480","C4489",
"C4490","C4499","C450","C451","C452","C457","C459","C460","C461",
"C462","C463","C464","C4650","C4651","C4652","C467","C469","C470",
"C4710","C4711","C4712","C4720","C4721","C4722","C473","C474",
"C475","C476","C478","C479","C480","C481","C482","C488","C490",
"C4910","C4911","C4912","C4920","C4921","C4922","C493","C494",
"C495","C496","C498","C499","C49A0","C49A1","C49A2","C49A3",
"C49A4","C49A5","C49A9","C4A0","C4A10","C4A11","C4A111",
"C4A112","C4A12","C4A121","C4A122","C4A20","C4A21","C4A22",
"C4A30","C4A31","C4A39","C4A4","C4A51","C4A52","C4A59","C4A60",
"C4A61","C4A62","C4A70","C4A71","C4A72","C4A8","C4A9","C50011",
"C50012","C50019","C50021","C50022","C50029","C50111","C50112",
"C50119","C50121","C50122","C50129","C50211","C50212","C50219",
"C50221","C50222","C50229","C50311","C50312","C50319","C50321",
"C50322","C50329","C50411","C50412","C50419","C50421","C50422",
"C50429","C50511","C50512","C50519","C50521","C50522","C50529",
"C50611","C50612","C50619","C50621","C50622","C50629","C50811",
"C50812","C50819","C50821","C50822","C50829","C50911","C50912",
"C50919","C50921","C50922","C50929","C510","C511","C512","C518",
"C519","C52","C530","C531","C538","C539","C540","C541","C542",
"C543","C548","C549","C55","C561","C562","C569","C5700","C5701",
"C5702","C5710","C5711","C5712","C5720","C5721","C5722","C573",
"C574","C577","C578","C579","C58","C600","C601","C602","C608",
"C609","C61","C6200","C6201","C6202","C6210","C6211","C6212","C6290",
"C6291","C6292","C6300","C6301","C6302","C6310","C6311","C6312","C632",
"C637","C638","C639","C641","C642","C649","C651","C652","C659","C661",
"C662","C669","C670","C671","C672","C673","C674","C675","C676","C677",
"C678","C679","C680","C681","C688","C689","C6900","C6901","C6902",
"C6910","C6911","C6912","C6920","C6921","C6922","C6930","C6931",
"C6932","C6940","C6941","C6942","C6950","C6951","C6952","C6960",
"C6961","C6962","C6980","C6981","C6982","C6990","C6991","C6992",
"C700","C701","C709","C710","C711","C712","C713","C714","C715",
"C716","C717","C718","C719","C720","C721","C7220","C7221","C7222",
"C7230","C7231","C7232","C7240","C7241","C7242","C7250","C7259",
"C729","C73","C7400","C7401","C7402","C7410","C7411","C7412",
"C7490","C7491","C7492","C750","C751","C752","C753","C754","C755",
"C758","C759","C760","C761","C762","C763","C7640","C7641","C7642",
"C7650","C7651","C7652","C768","C7A00","C7A010","C7A011","C7A012",
"C7A019","C7A020","C7A021","C7A022","C7A023","C7A024","C7A025",
"C7A026","C7A029","C7A090","C7A091","C7A092","C7A093","C7A094",
"C7A095","C7A096","C7A098","C7A1","C7A8","D469","E3121","E3122",
"E3123")
cbvd_poa10 <- c("G450","G451","G452","G453","G454","G458","G459","G460","G461",
"G462","G463","G464","G465","G466","G467","G468","H3400","H3401",
"H3402","H3403","H3410","H3411","H3412","H3413","H34211","H34212",
"H34213","H34219","H34231","H34232","H34233","H34239","I6000",
"I6001","I6002","I6010","I6011","I6012","I602","I6020","I6021",
"I6022","I6030","I6031","I6032","I604","I6050","I6051","I6052",
"I606","I607","I608","I609","I610","I611","I612","I613","I614",
"I615","I616","I618","I619","I6200","I6203","I621","I629",
"I6300","I63011","I63012","I63013","I63019","I6302","I63031",
"I63032","I63033","I63039","I6309","I6310","I63111","I63112",
"I63113","I63119","I6312","I63131","I63132","I63133","I63139",
"I6319","I6320","I63211","I63212","I63213","I63219","I6322",
"I63231","I63232","I63233","I63239","I6329","I6330","I63311",
"I63312","I63313","I63319","I63321","I63322","I63323","I63329",
"I63331","I63332","I63333","I63339","I63341","I63342","I63343",
"I63349","I6339","I6340","I63411","I63412","I63413","I63419",
"I63421","I63422","I63423","I63429","I63431","I63432","I63433",
"I63439","I63441","I63442","I63443","I63449","I6349","I6350",
"I63511","I63512","I63513","I63519","I63521","I63522","I63523",
"I63529","I63531","I63532","I63533","I63539","I63541","I63542",
"I63543","I63549","I6359","I636","I638","I6381","I6389","I639",
"I6501","I6502","I6503","I6509","I651","I6521","I6522","I6523",
"I6529","I658","I659","I6601","I6602","I6603","I6609","I6611",
"I6612","I6613","I6619","I6621","I6622","I6623","I6629","I663",
"I668","I669")
cbvd_sqla10 <- c("I6930","I6931","I69310","I69311","I69312","I69313","I69314",
"I69315","I69318","I69319","I69320","I69321","I69322","I69323",
"I69328","I69390","I69391","I69392","I69393","I69398","I6980",
"I6981","I69810","I69811","I69812","I69813","I69814","I69815",
"I69818","I69819","I69820","I69821","I69822","I69823","I69828",
"I69890","I69891","I69892","I69893","I69898","I6990","I6991",
"I69910","I69911","I69912","I69913","I69914","I69915","I69918",
"I69919","I69920","I69921","I69922","I69923","I69928","I69990",
"I69991","I69992","I69993","I69998","P91821","P91822","P91823",
"P91829")
cbvd_sqlaparalysis10 <- c("I69331","I69332","I69333","I69334","I69339","I69341",
"I69342","I69343","I69344","I69349","I69351","I69352",
"I69353","I69354","I69359","I69361","I69362","I69363",
"I69364","I69365","I69369","I69831","I69832","I69833",
"I69834","I69839","I69841","I69842","I69843","I69844",
"I69849","I69851","I69852","I69853","I69854","I69859",
"I69861","I69862","I69863","I69864","I69865","I69869",
"I69931","I69932","I69933","I69934","I69939","I69941",
"I69942","I69943","I69944","I69949","I69951","I69952",
"I69953","I69954","I69959","I69961","I69962","I69963",
"I69964","I69965","I69969")
chf10 <- c("I0981","I501","I5020","I5021","I5022","I5023","I5030","I5031","I5032",
"I5033","I5040","I5041","I5042","I5043","I50810","I50811","I50812",
"I50813","I50814","I5082","I5083","I5084","I5089","I509","I5181",
"I97130","I97131","O29121","O29122","O29123","O29129","R570",
"Z95811","Z95812")
chfhtn_cx10 <- c("I110", "I130")
chfhtn_cxrenfl_sev10 <- c("I132")
coag10 <- c("D6109","D611","D612","D613","D61810","D61811","D61818","D6182",
"D6189","D619","D65","D66","D67","D680","D681","D682","D68311",
"D68312","D68318","D6832","D684","D688","D689","D691","D693",
"D6941","D6942","D6949","D6951","D6959","D696","D698","D699",
"D7582","O99111","O99112","O99113","O99119","O9912","O9913")
dementia10 <- c("F0150","F0151","F0280","F0281","F0390","F0391","G300","G301",
"G308","G309","G3101","G3109","G311","G312","G3181","G3182",
"G3183","G3185","G3189","G319")
depress10 <- c("F0631","F0632","F0634","F320","F321","F322","F323","F328",
"F3281","F3289","F329","F330","F331","F332","F333","F338",
"F339","F341")
diab_c10 <- c("E0821","E0822","E0829","E08311","E08319","E08321","E083211",
"E083212","E083213","E083219","E08329","E083291","E083292",
"E083293","E083299","E08331","E083311","E083312","E083313",
"E083319","E08339","E083391","E083392","E083393","E083399",
"E08341","E083411","E083412","E083413","E083419","E08349",
"E083491","E083492","E083493","E083499","E08351","E083511",
"E083512","E083513","E083519","E083521","E083522","E083523",
"E083529","E083531","E083532","E083533","E083539","E083541",
"E083542","E083543","E083549","E083551","E083552","E083553",
"E083559","E08359","E083591","E083592","E083593","E083599",
"E0836","E0837X1","E0837X2","E0837X3","E0837X9","E0839","E0840",
"E0841","E0842","E0843","E0844","E0849","E0851","E0852","E0859",
"E08610","E08618","E08620","E08621","E08622","E08628","E08630",
"E08638","E08641","E08649","E0865","E0869","E088","E0921","E0922",
"E0929","E09311","E09319","E09321","E093211","E093212","E093213","
E093219","E09329","E093291","E093292","E093293","E093299","E09331",
"E093311","E093312","E093313","E093319","E09339","E093391","E093392",
"E093393","E093399","E09341","E093411","E093412","E093413","E093419",
"E09349","E093491","E093492","E093493","E093499","E09351","E093511",
"E093512","E093513","E093519","E093521","E093522","E093523","E093529",
"E093531","E093532","E093533","E093539","E093541","E093542","E093543",
"E093549","E093551","E093552","E093553","E093559","E09359","E093591",
"E093592","E093593","E093599","E0936","E0937X1","E0937X2","E0937X3",
"E0937X9","E0939","E0940","E0941","E0942","E0943","E0944","E0949",
"E0951","E0952","E0959","E09610","E09618","E09620","E09621",
"E09622","E09628","E09630","E09638","E09641","E09649","E0965",
"E0969","E098","E1021","E1022","E1029","E10311","E10319","E10321",
"E103211","E103212","E103213","E103219","E10329","E103291","E103292",
"E103293","E103299","E10331","E103311","E103312","E103313","E103319",
"E10339","E103391","E103392","E103393","E103399","E10341","E103411",
"E103412","E103413","E103419","E10349","E103491","E103492","E103493",
"E103499","E10351","E103511","E103512","E103513","E103519","E103521",
"E103522","E103523","E103529","E103531","E103532","E103533","E103539",
"E103541","E103542","E103543","E103549","E103551","E103552","E103553",
"E103559","E10359","E103591","E103592","E103593","E103599","E1036",
"E1037X1","E1037X2","E1037X3","E1037X9","E1039","E1040","E1041",
"E1042","E1043","E1044","E1049","E1051","E1052","E1059","E10610",
"E10618","E10620","E10621","E10622","E10628","E10630","E10638",
"E10641","E10649","E1065","E1069","E108","E1121","E1122","E1129",
"E11311","E11319","E11321","E113211","E113212","E113213","E113219",
"E11329","E113291","E113292","E113293","E113299","E11331","E113311",
"E113312","E113313","E113319","E11339","E113391","E113392","E113393",
"E113399","E11341","E113411","E113412","E113413","E113419","E11349",
"E113491","E113492","E113493","E113499","E11351","E113511","E113512",
"E113513","E113519","E113521","E113522","E113523","E113529","E113531",
"E113532","E113533","E113539","E113541","E113542","E113543","E113549",
"E113551","E113552","E113553","E113559","E11359","E113591","E113592",
"E113593","E113599","E1136","E1137X1","E1137X2","E1137X3","E1137X9",
"E1139","E1140","E1141","E1142","E1143","E1144","E1149","E1151",
"E1152","E1159","E11610","E11618","E11620","E11621","E11622","
E11628","E11630","E11638","E11641","E11649","E1165","E1169","E118",
"E1321","E1322","E1329","E13311","E13319","E13321","E133211","E133212",
"E133213","E133219","E13329","E133291","E133292","E133293","E133299",
"E13331","E133311","E133312","E133313","E133319","E13339","E133391",
"E133392","E133393","E133399","E13341","E133411","E133412","E133413",
"E133419","E13349","E133491","E133492","E133493","E133499","E13351",
"E133511","E133512","E133513","E133519","E133521","E133522","E133523",
"E133529","E133531","E133532","E133533","E133539","E133541","E133542",
"E133543","E133549","E133551","E133552","E133553","E133559","E13359",
"E133591","E133592","E133593","E133599","E1336","E1337X1","E1337X2",
"E1337X3","E1337X9","E1339","E1340","E1341","E1342","E1343","E1344",
"E1349","E1351","E1352","E1359","E13610","E13618","E13620","E13621",
"E13622","E13628","E13630","E13638","E13641","E13649","E1365","E1369",
"E138")
diab_uc10 <- c("E0800","E0801","E0810","E0811","E089","E0900","E0901","E0910",
"E0911","E099","E1010","E1011","E109","E1100","E1101","E1110",
"E1111","E119","E1300","E1301","E1310","E1311","E139","O24011",
"O24012","O24013","O24019","O2402","O2403","O24111","O24112",
"O24113","O24119","O2412","O2413","O24311","O24312","O24313",
"O24319","O2432","O2433","O24410","O24414","O24415","O24419",
"O24420","O24424","O24425","O24429","O24430","O24434","O24435",
"O24439","O24811","O24812","O24813","O24819","O2482","O2483",
"O24911","O24912","O24913","O24919","O2492","O2493")
drug10 <- c("F1110","F1111","F11120","F11121","F11122","F11129","F1113","F1114",
"F11181","F11182","F11188","F1119","F1120","F1121","F11220","F11221",
"F11222","F11229","F1123","F1124","F11281","F11282","F11288","F1129",
"F1210","F1211","F12120","F12121","F12122","F12129","F1213","F12180",
"F12188","F1219","F1220","F1221","F12220","F12221","F12222","F12229",
"F1223","F12280","F12288","F1229","F1310","F1311","F13120","F13121",
"F13129","F13130","F13131","F13132","F13139","F1314","F13180","F13181",
"F13182","F13188","F1319","F1320","F1321","F13220","F13221","F13229",
"F13230","F13231","F13232","F13239","F1324","F1326","F1327","F13280",
"F13281","F13282","F13288","F1329","F1410","F1411","F14120","F14121",
"F14122","F14129","F1413","F1414","F14180","F14181","F14182","F14188",
"F1419","F1420","F1421","F14220","F14221","F14222","F14229","F1423",
"F1424","F14280","F14281","F14282","F14288","F1429","F1510","F1511",
"F15120","F15121","F15122","F15129","F1513","F1514","F15180","F15181",
"F15182","F15188","F1519","F1520","F1521","F15220","F15221","F15222",
"F15229","F1523","F1524","F15280","F15281","F15282","F15288","F1529",
"F1610","F1611","F16120","F16121","F16122","F16129","F1614","F16180",
"F16183","F16188","F1619","F1620","F1621","F16220","F16221","F16229",
"F1624","F16280","F16283","F16288","F1629","F1810","F1811","F18120",
"F18121","F18129","F1814","F1817","F18180","F18188","F1819","F1820",
"F1821","F18220","F18221","F18229","F1824","F1827","F18280","F18288",
"F1829","F1910","F1911","F19120","F19121","F19122","F19129","F19130",
"F19131","F19132","F19139","F1914","F1916","F1917","F19180","F19181",
"F19182","F19188","F1919","F1920","F1921","F19220","F19221","F19222",
"F19229","F19230","F19231","F19232","F19239","F1924","F1926","F1927",
"F19280","F19281","F19282","F19288","F1929","O99320","O99321",
"O99322","O99323","O99324","O99325")
drug_psych10 <- c("F11150","F11151","F11159","F11250","F11251","F11259",
"F12150","F12151","F12159","F12250","F12251","F12259",
"F13150","F13151","F13159","F13250","F13251","F13259",
"F14150","F14151","F14159","F14250","F14251","F14259",
"F15150","F15151","F15159","F15250","F15251","F15259",
"F16150","F16151","F16159","F16250","F16251","F16259",
"F18150","F18151","F18159","F18250","F18251","F18259",
"F19150","F19151","F19159","F19250","F19251","F19259")
htn_c10 <- c("H35031","H35032","H35033","H35039","I119","I129","I1310","I150",
"I151","I152","I158","I159","I161","I674","O10111","O10112",
"O10113","O10119","O1012","O1013","O10211","O10212","O10213",
"O10219","O1022","O1023","O10311","O10312","O10313","O10319",
"O1032","O1033","O10411","O10412","O10413","O10419","O1042",
"O1043","O10911","O10912","O10913","O10919","O1092","O1093",
"O111","O112","O113","O114","O115","O119","O161","O162","O163",
"O164","O165","O169")
htn_cxrenlfl_sv10 <- c("I120", "I1311")
htn_uc10 <- c("I10","I160","I169","O10011","O10012","O10013","O10019","O1002",
"O1003")
liver_mild10 <- c("A5145","A5274","B180","B181","B182","B188","B189","B1910",
"B1920","B199","B251","B581","K700","K702","K7030","K7031",
"K709","K713","K714","K7150","K7151","K716","K717","K718",
"K730","K731","K732","K738","K739","K740","K7400","K7401",
"K7402","K741","K742","K743","K744","K745","K7460","K7469",
"K751","K752","K753","K754","K7581","K7589","K759","K760",
"K761","K762","K763","K764","K7681","K7689","K769","K77")
liver_sev10 <- c("B190","B1911","B1921","I8500","I8501","I8510","I8511","I864",
"K7040","K7041","K7210","K7211","K7290","K7291","K765","K766",
"K767","K9182","Z944")
chronic_pulm10 <- c("J410","J411","J418","J42","J430","J431","J432","J438",
"J439","J440","J441","J449","J4520","J4521","J4522",
"J4530","J4531","J4532","J4540","J4541","J4542","J4550",
"J4551","J4552","J45901","J45902","J45909","J45990",
"J45991","J45998","J470","J471","J479","J60","J61",
"J620","J628","J630","J631","J632","J633","J634",
"J635","J636","J64","J65","J660","J661","J662","J668","J670",
"J671","J672","J673","J674","J675","J676","J677","J678",
"J679","J684","J701","J703")
neuro_mvt10 <- c("G08","G10","G110","G111","G1110","G1111","G1119","G112",
"G113","G114","G118","G119","G120","G121","G1220","G1221",
"G1222","G1223","G1224","G1225","G1229","G128","G129","G130",
"G131","G132","G138","G20","G210","G2111","G2119","G212",
"G213","G214","G218","G219","G230","G231","G232","G238",
"G239","G2409","G241","G242","G248","G254","G255","G2570",
"G2571","G2579","G2581","G2582","G2583","G2589","G259","G26",
"G320","G3281","G3289","G803")
neuro_oth10 <- c("E7500","E7501","E7502","E7509","E7510","E7511","E7519","E7523",
"E7525","E7526","E7529","E754","F05","F842","G35","G360","G368",
"G369","G370","G371","G372","G373","G374","G375","G378","G379",
"G47411","G47419","G47421","G47429","G890","G910","G911","G912",
"G913","G914","G918","G919","G930","G9340","G9341","G9349",
"G935","G936","G937","G9381","G9382","G9389","G939","G94",
"O99350","O99351","O99352","O99353","O99354","O99355","P9160",
"P9161","P9162","P9163")
neuro_seiz10 <- c("G40001","G40009","G40011","G40019","G40101","G40109","G40111",
"G40119","G40201","G40209","G40211","G40219","G40301","G40309",
"G40311","G40319","G40401","G40409","G40411","G40419","G4042",
"G40501","G40509","G40801","G40802","G40803","G40804","G40811",
"G40812","G40813","G40814","G40821","G40822","G40823","G40824",
"G40833","G40834","G4089","G40901","G40909","G40911","G40919",
"G40A01","G40A09","G40A11","G40A19","G40B01","G40B09","G40B11",
"G40B19","R561","R569")
obese10 <- c("E6601","E6609","E661","E662","E668","E669","O99210","O99211",
"O99212","O99213","O99214","O99215","R939","Z6830","Z6831","Z6832",
"Z6833","Z6834","Z6835","Z6836","Z6837","Z6838","Z6839","Z6841",
"Z6842","Z6843","Z6844","Z6845","Z6854")
paralysis10 <- c("G041","G800","G801","G802","G808","G809","G8100","G8101",
"G8102","G8103","G8104","G8110","G8111","G8112","G8113",
"G8114","G8190","G8191","G8192","G8193","G8194","G8220","G8221",
"G8222","G8250","G8251","G8252","G8253","G8254","G830","G8310",
"G8311","G8312","G8313","G8314","G8320","G8321","G8322","G8323",
"G8324","G8330","G8331","G8332","G8333","G8334","G834","G835",
"G8381","G8382","G8383","G8384","G8389","G839","I69031",
"I69032","I69033","I69034","I69039","I69041","I69042","I69043",
"I69044","I69049","I69051","I69052","I69053","I69054","I69059",
"I69061","I69062","I69063","I69064","I69065","I69069","I69131",
"I69132","I69133","I69134","I69139","I69141","I69142","I69143",
"I69144","I69149","I69151","I69152","I69153","I69154","I69159",
"I69161","I69162","I69163","I69164","I69165","I69169","I69231",
"I69232","I69233","I69234","I69239","I69241","I69242","I69243",
"I69244","I69249","I69251","I69252","I69253","I69254","I69259",
"I69261","I69262","I69263","I69264","I69265","I69269","R532")
periph_vasc10 <- c("A5200","A5201","A5202","A5209","I700","I701","I70201",
"I70202","I70203","I70208","I70209","I70211","I70212",
"I70213","I70218","I70219","I70221","I70222","I70223",
"I70228","I70229","I70231","I70232","I70233","I70234",
"I70235","I70238","I70239","I70241","I70242","I70243",
"I70244","I70245","I70248","I70249","I7025","I70261",
"I70262","I70263","I70268","I70269","I70291","I70292",
"I70293","I70298","I70299","I70301","I70302","I70303",
"I70308","I70309","I70311","I70312","I70313","I70318",
"I70319","I70321","I70322","I70323","I70328","I70329",
"I70331","I70332","I70333","I70334","I70335","I70338",
"I70339","I70341","I70342","I70343","I70344","I70345",
"I70348","I70349","I7035","I70361","I70362","I70363",
"I70368","I70369","I70391","I70392","I70393","I70398",
"I70399","I70401","I70402","I70403","I70408","I70409",
"I70411","I70412","I70413","I70418","I70419","I70421",
"I70422","I70423","I70428","I70429","I70431","I70432",
"I70433","I70434","I70435","I70438","I70439","I70441",
"I70442","I70443","I70444","I70445","I70448","I70449",
"I7045","I70461","I70462","I70463","I70468","I70469",
"I70491","I70492","I70493","I70498","I70499","I70501",
"I70502","I70503","I70508","I70509","I70511","I70512",
"I70513","I70518","I70519","I70521","I70522","I70523",
"I70528","I70529","I70531","I70532","I70533","I70534",
"I70535","I70538","I70539","I70541","I70542","I70543",
"I70544","I70545","I70548","I70549","I7055","I70561",
"I70562","I70563","I70568","I70569","I70591","I70592",
"I70593","I70598","I70599","I70601","I70602","I70603",
"I70608","I70609","I70611","I70612","I70613","I70618",
"I70619","I70621","I70622","I70623","I70628","I70629",
"I70631","I70632","I70633","I70634","I70635","I70638",
"I70639","I70641","I70642","I70643","I70644","I70645",
"I70648","I70649","I7065","I70661","I70662","I70663",
"I70668","I70669","I70691","I70692","I70693","I70698",
"I70699","I70701","I70702","I70703","I70708","I70709",
"I70711","I70712","I70713","I70718","I70719","I70721",
"I70722","I70723","I70728","I70729","I70731","I70732",
"I70733","I70734","I70735","I70738","I70739","I70741",
"I70742","I70743","I70744","I70745","I70748","I70749",
"I7075","I70761","I70762","I70763","I70768","I70769",
"I70791","I70792","I70793","I70798","I70799","I708",
"I7090","I7091","I7092","I7100","I7101","I7102","I7103",
"I711","I712","I713","I714","I715","I716","I718","I719",
"I720","I721","I722","I723","I724","I725","I726","I728",
"I729","I7301","I731","I7381","I7389","I739","I7401",
"I7409","I7410","I7411","I7419","I742","I743","I744",
"I745","I748","I749","I75011","I75012","I75013","I75019",
"I75021","I75022","I75023","I75029","I7581","I7589","I770",
"I771","I772","I773","I774","I775","I776","I7770","I7771",
"I7772","I7773","I7774","I7775","I7776","I7777","I7779",
"I77810","I77811","I77812","I77819","I7789","I779","I780",
"I781","I788","I789","I790","I791","I798","I998","I999",
"K31811","K31819","K551","K558","K559","Z95820","Z95828")
psych10 <- c("F060","F061","F062","F0630","F0633","F11950","F11951","F11959",
"F12950","F12951","F12959","F13950","F13951","F13959","F14950",
"F14951","F14959","F15950","F15951","F15959","F16950","F16951",
"F16959","F18950","F18951","F18959","F19950","F19951","F19959",
"F200","F201","F202","F203","F205","F2081","F2089","F209","F21",
"F22","F23","F24","F250","F251","F258","F259","F28","F29","F3010",
"F3011","F3012","F3013","F302","F303","F304","F308","F309","F310",
"F3110","F3111","F3112","F3113","F312","F3130","F3131","F3132",
"F314","F315","F3160","F3161","F3162","F3163","F3164","F3170",
"F3171","F3172","F3173","F3174","F3175","F3176","F3177","F3178",
"F3181","F3189","F319","F324","F325","F3340","F3341","F3342",
"F340","F348","F3481","F3489","F349","F39","F4489","F843")
pulmcirc10 <- c("I270","I271","I272","I2720","I2721","I2722","I2723","I2724",
"I2729","I2781","I2782","I2783","I2789","I279","I280","I281",
"I288","I289")
renal_mod10 <- c("N183","N1830","N1831","N1832","N189","N19")
renal_sev10 <- c("N184","N185","N186","Z4901","Z4902","Z4931","Z4932","Z9115",
"Z940","Z992")
hypo10 <- c("E000","E001","E002","E009","E010","E011","E012","E018","E02",
"E030","E031","E032","E033","E034","E035","E038","E039","E890")
thy_oth10 <- c("E040","E041","E042","E048","E049","E0500","E0501","E0510",
"E0511","E0520","E0521","E0530","E0531","E0540","E0541","E0580",
"E0581","E0590","E0591","E060","E061","E062","E063","E064",
"E065","E069","O905")
peptic10 <- c("K250","K251","K252","K253","K254","K255","K256","K257","K259",
"K260","K261","K262","K263","K264","K265","K266","K267","K269",
"K270","K271","K272","K273","K274","K275","K276","K277","K279",
"K280","K281","K282","K283","K284","K285","K286","K287","K289")
valve10 <- c("A1884","A3282","A3951","A5203","B3321","B376","I011","I018",
"I019","I020","I050","I051","I052","I058","I059","I060","I061",
"I062","I068","I069","I070","I071","I072","I078","I079","I080",
"I081","I082","I083","I088","I089","I091","I0989","I330","I339",
"I340","I341","I342","I348","I349","I350","I351","I352","I358",
"I359","I360","I361","I362","I368","I369","I370","I371","I372",
"I378","I379","I38","I39","M3211","Q220","Q221","Q222","Q223",
"Q224","Q225","Q226","Q228","Q229","Q230","Q231","Q232","Q233",
"Q234","Q238","Q239","T8201XA","T8201XD","T8201XS","T8202XA",
"T8202XD","T8202XS","T8203XA","T8203XD","T8203XS","T8209XA",
"T8209XD","T8209XS","T82221A","T82221D","T82221S","T82222A",
"T82222D","T82222S","T82223A","T82223D","T82223S","T82228A",
"T82228D","T82228S","T826XXA","T826XXD","T826XXS","Z952",
"Z953","Z954")
weightloss10 <- c("E40","E41","E42","E43","E440","E441","E45","E46","E640","O2510",
"O2511","O2512","O2513","O252","O253","R634","R64")
# Code ----
dat1 <- dat %>%
dplyr::mutate(aids = dplyr::if_else(dx %in% hiv10, 1, 0),
alcohol = dplyr::if_else(dx %in% alcohol10 | dx %in% alcohol_liver_mild10, 1, 0),
def_anem = dplyr::if_else(dx %in% def_anem10, 1, 0),
rheum = dplyr::if_else(dx %in% rheum10, 1, 0),
bld_loss = dplyr::if_else(dx %in% bld_loss10, 1, 0),
cancer_leuk = dplyr::if_else(dx %in% leuk10, 1, 0),
cancer_lymph = dplyr::if_else(dx %in% lymph10, 1, 0),
cancer_mets = dplyr::if_else(dx %in% mets10, 1, 0),
cancer_solid = dplyr::if_else(dx %in% solid10, 1, 0),
cancer_insitu = dplyr::if_else(dx %in% insitu10, 1, 0),
cbvd = dplyr::if_else(dx %in% cbvd_poa10 | dx %in% cbvd_sqla10, 1, 0),
chf = dplyr::if_else(dx %in% chf10, 1, 0),
coag = dplyr::if_else(dx %in% coag10, 1, 0),
dementia = dplyr::if_else(dx %in% dementia10, 1, 0),
depress = dplyr::if_else(dx %in% depress10, 1, 0),
diab_c = dplyr::if_else(dx %in% diab_c10, 1, 0),
diab_uc = dplyr::if_else(dx %in% diab_uc10, 1, 0),
drug = dplyr::if_else(dx %in% drug10 | dx %in% drug_psych10, 1, 0),
htn_c = dplyr::if_else(dx %in% htn_c10 | dx %in% chfhtn_cx10 | dx %in% chfhtn_cxrenfl_sev10, 1, 0),
htn_uc = dplyr::if_else(dx %in% htn_uc10, 1, 0),
liver_mild = dplyr::if_else(dx %in% liver_mild10, 1, 0),
liver_sev = dplyr::if_else(dx %in% liver_sev10, 1, 0),
chronic_pulm = dplyr::if_else(dx %in% chronic_pulm10, 1, 0),
neuro_movt = dplyr::if_else(dx %in% neuro_mvt10, 1, 0),
neuro_seiz = dplyr::if_else(dx %in% neuro_seiz10, 1, 0),
neuro_oth = dplyr::if_else(dx %in% neuro_oth10, 1, 0),
obese = dplyr::if_else(dx %in% obese10, 1, 0),
paralysis = dplyr::if_else(dx %in% paralysis10 | dx %in% cbvd_sqlaparalysis10, 1, 0),
perivasc = dplyr::if_else(dx %in% periph_vasc10, 1, 0),
psych = dplyr::if_else(dx %in% psych10, 1, 0),
pulmcirc = dplyr::if_else(dx %in% pulmcirc10, 1, 0),
renal_mod = dplyr::if_else(dx %in% renal_mod10, 1, 0),
renal_sev = dplyr::if_else(dx %in% renal_sev10, 1, 0),
hypo = dplyr::if_else(dx %in% hypo10, 1, 0),
thyroid_oth = dplyr::if_else(dx %in% thy_oth10, 1, 0),
peptic = dplyr::if_else(dx %in% peptic10, 1, 0),
valve = dplyr::if_else(dx %in% valve10, 1, 0),
weightloss = dplyr::if_else(dx %in% weightloss10, 1, 0))
dat1 <- dat1 %>%
dplyr::mutate(diab_uc = dplyr::if_else(.data$diab_c == 1, 0, .data$diab_uc),
htn_uc = dplyr::if_else(.data$htn_c == 1, 0, .data$htn_c),
cancer_solid = dplyr::if_else(.data$cancer_mets == 1, 0, .data$cancer_solid),
cancer_insitu = dplyr::if_else(.data$cancer_mets == 1, 0, .data$cancer_insitu),
cancer_insitu = dplyr::if_else(.data$cancer_solid == 1, 0, .data$cancer_insitu),
liver_mild = dplyr::if_else(.data$liver_sev == 1, 0, .data$liver_mild),
renal_mild = dplyr::if_else(.data$renal_sev == 1, 0, .data$renal_sev))
}
# Elixhauser Both ----
else if (version == 19){
message("Message: Specifying that your data uses both ICD-9 and ICD-10 will result in only the Elixhauser comorbidities \n which are compatible with ICD-9, as the changes and additions which are seen in \n ICD-10 have, to date, not been back-mapped to ICD-9.")
## Diagnoses Setup ----
chf9 <- c("39891", "40201", "40211", "40291", "40401", "40403", "40411", "40413", "40491", "40493",
"4254", "4255", "4257", "4258", "4259")
valve9 <- c("3979", "V422", "V433", "7463", "7464", "7465", "7466")
pulmcirc9 <- c("4179")
periph_vasc9 <- c("44421", "44422", "4471", "449", "4471", "5571", "5579", "V434")
paralysis9 <- c("3449", "78072")
neuro9 <- c("3334", "3335", "33385", "33394", "3452", "3453", "78097", "7843")
chronic_pulm9 <- c("5064")
diab_c9 <- c("7751")
hypo9 <- c("243", "2440", "2441", "2442", "2448", "2449")
renal9 <- c("5853", "5854 ", "5855 ", "5856 ", "5859 ", "586", "V420", "V451", "V4511", "V4512")
liver9 <- c("07022", "07023", "07032", "07033", "07044", "07054", "4560",
"4561", "45620", "45621", "5710", "5712 ", "5713", "5715", "5716",
"5718", "5719", "5723", "5728", "5735", "V427")
peptic9 <- c("53141", "53151", "53161", "53170", "53171", "53191", "53241",
"53251", "53261", "53270", "53271", "53291", "53341", "53351",
"53361", "53370", "53371", "53391", "53441", "53451", "53461",
"53470", "53471", "53491")
mets9 <- c("1990", "1991", "78951")
rheum9 <- c("7010")
coag9 <- c("2871", "28984")
obese9 <- c("2780", "V8554", "79391")
weightloss9 <- c("78321", "78322")
bld_anem9 <- c("2800")
alc9 <- c("2910", "2911", "2912", "2913", "2915", "2919")
drug9 <- c("2920", "2929")
depress9 <- c("3004", "30112", "3090", "3091", "311")
chf9_str <- ("428")
valve9_str <- c("424", "0932", "394", "395", "396", "397")
pulmcirc9_str <- c("4151", "416")
periph_vasc9_str <- c("440", "441", "442", "4431", "4432", "4438", "4439")
htn_uc9_str <- c("4011", "4019", "6420")
htn_c9_str <- c("402", "403", "404", "405", "6422", "6421", "6427", "6429")
paralysis9_str <- c("342", "343", "3440", "3441", "3442", "3443", "3444", "3445", "3446", "4382", "4383", "4384", "4385")
neuro9_str <- c("330", "331", "332", "3337", "3334", "3335", "3338", "340", "341","3450", "3451", "3454", "3455", "3456",
"3457", "3458", "3459", "347", "6494", "7687", "7803")
chronic_pulm9_str <- c("490", "491", "492", "493", "494", "495", "496", "500", "501", "502")
diab_uc9_str <- c("2500", "2501", "2502", "2503", "6480", "2490", "2491", "2492", "2493")
diab_c9_str <- c("2504", "2505", "2506", "2507", "2508", "2509", "2494", "2495", "2496", "2497", "2498", "2499")
renal9_str <- c("V560", "V561", "V562", "V563", "V568")
liver9_str <- c("5714")
hiv9_str <- c("042", "043", "044")
lymph9_str <- c("200", "201", "2020", "2021", "2022", "2025", "2026", "2027", "2028", "2029", "203", "2386", "2733")
mets9_str <- c("196", "197", "198", "209")
tumor9_str <- c("14, 15, 16, 170", "171", "172", "174", "175", "179",
"18", "190", "191", "192", "193", "194", "195", "2090", "2091", "2092", "2093", "2580")
rheum9_str <- c("710", "714", "720", "725")
coag9_str <- c("286", "2873", "2874", "2875", "6493")
obese9_str <- c("2780", "6491", "V853", "V854")
weightloss9_str <- c("260", "261", "262", "263")
fluid9_str <- c("276")
bld_anem9_str <- c("6482")
def_anem9_str <- c("280", "2852", "2859")
alcohol9_str <- c("2918", "303", "3050")
drug9_str <- c("2928", "304", "3052", "3053", "3054", "3055", "3056", "3057", "3058", "3059", "6483")
psych9_str <- c("295", "296", "297", "298", "2991")
chf10beta <- c("I0981","I501","I5020","I5021","I5022","I5023","I5030",
"I5031","I5032","I5033","I5040","I5041","I5042","I5043",
"I50810","I50811","I50812","I50813","I50814","I5082",
"I5083","I5084","I5089","I509","I130") # hhrwchf
valve10beta <- c("A5203","I050","I051","I052","I058","I059","I060","I061",
"I062","I068","I069","I070","I071","I072","I078","I079",
"I080","I081","I082","I083","I088","I089","I091","I0989",
"I340","I341","I342","I348","I349","I350","I351","I352",
"I358","I359","I360","I361","I362","I368","I369","I370",
"I371","I372","I378","I379","I38","I39","Q230","Q231",
"Q232","Q233","Z952","Z953","Z954")
pulmcirc10beta <- c("I2601","I2602","I2609","I2690","I2692","I2693",
"I2694","I2699","I270","I271","I2781","I2782","I2783",
"I2789","I279","I289","T800XXA","T82817A","T82818A")
periph_vasc10beta <- c("I700","I701","I70201","I70202","I70203","I70208",
"I70209","I70211","I70212","I70213","I70218","I70219",
"I70221","I70222","I70223","I70228","I70229","I70231",
"I70232","I70233","I70234","I70235","I70238","I70239",
"I70241","I70242","I70243","I70244","I70245","I70248",
"I70249","I7025","I70261","I70262","I70263","I70268",
"I70269","I70291","I70292","I70293","I70298","I70299",
"I70301","I70302","I70303","I70308","I70309","I70311",
"I70312","I70313","I70318","I70319","I70321","I70322",
"I70323","I70328","I70329","I70331","I70332","I70333",
"I70334","I70335","I70338","I70339","I70341","I70342",
"I70343","I70344","I70345","I70348","I70349","I7035",
"I70361","I70362","I70363","I70368","I70369","I70391",
"I70392","I70393","I70398","I70399","I70401","I70402",
"I70403","I70408","I70409","I70411","I70412","I70413",
"I70418","I70419","I70421","I70422","I70423","I70428",
"I70429","I70431","I70432","I70433","I70434","I70435",
"I70438","I70439","I70441","I70442","I70443","I70444",
"I70445","I70448","I70449","I7045","I70461","I70462",
"I70463","I70468","I70469","I70491","I70492","I70493",
"I70498","I70499","I70501","I70502","I70503","I70508",
"I70509","I70511","I70512","I70513","I70518","I70519",
"I70521","I70522","I70523","I70528","I70529","I70531",
"I70532","I70533","I70534","I70535","I70538","I70539",
"I70541","I70542","I70543","I70544","I70545","I70548",
"I70549","I7055","I70561","I70562","I70563","I70568",
"I70569","I70591","I70592","I70593","I70598","I70599",
"I70601","I70602","I70603","I70608","I70609","I70611",
"I70612","I70613","I70618","I70619","I70621","I70622",
"I70623","I70628","I70629","I70631","I70632","I70633",
"I70634","I70635","I70638","I70639","I70641","I70642",
"I70643","I70644","I70645","I70648","I70649","I7065",
"I70661","I70662","I70663","I70668","I70669","I70691",
"I70692","I70693","I70698","I70699","I70701","I70702",
"I70703","I70708","I70709","I70711","I70712","I70713",
"I70718","I70719","I70721","I70722","I70723","I70728"
,"I70729","I70731","I70732","I70733","I70734","I70735",
"I70738","I70739","I70741","I70742","I70743","I70744",
"I70745","I70748","I70749","I7075","I70761","I70762",
"I70763","I70768","I70769","I70791","I70792","I70793",
"I70798","I70799","I708","I7090","I7091","I7092","I7100",
"I7101","I7102","I7103","I711","I712","I713","I714",
"I715","I716","I718","I719","I720","I721","I722","I723",
"I724","I725","I726","I728","I729","I731","I7381",
"I7389","I739","I742","I743","I744","I76","I771",
"I7770","I7771","I7772","I7773","I7774","I7775",
"I7776","I7777","I7779","I790","I791","I798","K551",
"K558","K559","Z95820","Z95828")
htn_uc10beta <- c("I10", "O10011","O10012","O10013","O10019","O1002","O1003",
"O10911","O10912","O10913","O10919","O1092","O1093")
htn_c10beta <- c("I160","I161","I169","I674",
"I130", # hhrwchf
"I1310", # hhrwohrf
"I129", #hrenworf
"I150", #hrenworf
"I151", #hrenworf
"I120", #hrnwrf
"O10111", #htnpreg
"O10112","O10113","O10119","O1012","O1013","O10211",
"O10212","O10213","O10219","O1022","O1023","O10311",
"O10312","O10313","O10319","O1032","O1033","O10411",
"O10412","O10413","O10419","O1042","O1043","O111","O112",
"O113","O114","O115","O119",
"O161", # ohtnpreg
"O162",
"O163",
"O164",
"O165",
"O169",
"I110", #htnwchf
"I110", #htnwchf
"I119", #htnwochf
"I152", "I158", "I159")
paralysis10beta <- c("G041","G800","G801","G802","G804","G808","G809",
"G8100","G8101","G8102","G8103","G8104","G8110",
"G8111","G8112","G8113","G8114","G8190","G8191",
"G8192","G8193","G8194","G8220","G8221","G8222",
"G8250","G8251","G8252","G8253","G8254","G830","
G8310","G8311","G8312","G8313","G8314","G8320","G8321",
"G8322","G8323","G8324","G8330","G8331","G8332","G8333",
"G8334","G834","G835","G8381","G8382","G8383","G8384",
"G8389","G839","I69031","I69032","I69033","I69034",
"I69039","I69041","I69042","I69043","I69044","I69049",
"I69051","I69052","I69053","I69054","I69059","I69061",
"I69062","I69063","I69064","I69065","I69069","I69131","
I69132","I69133","I69134","I69139","I69141","I69142",
"I69143","I69144","I69149","I69151","I69152","I69153",
"I69154","I69159","I69161","I69162","I69163","I69164",
"I69165","I69169","I69231","I69232","I69233","I69234",
"I69239","I69241","I69242","I69243","I69244","I69249",
"I69251","I69252","I69253","I69254","I69259","I69261",
"I69262","I69263","I69264","I69265","I69269","I69331",
"I69332","I69333","I69334","I69339","I69341","I69342",
"I69343","I69344","I69349","I69351","I69352","I69353",
"I69354","I69359","I69361","I69362","I69363","I69364",
"I69365","I69369","I69831","I69832","I69833","I69834",
"I69839","I69841","I69842","I69843","I69844","I69849",
"I69851","I69852","I69853","I69854","I69859","I69861",
"I69862","I69863","I69864","I69865","I69869","I69931",
"I69932","I69933","I69934","I69939","I69941","I69942",
"I69943","I69944","I69949","I69951","I69952","I69953",
"I69954","I69959","I69961","I69962","I69963","I69964",
"I69965","I69969","R532")
neuro10beta <- c("E7500","E7501","E7502","E7509","E7510","E7511","E7519",
"E7523","E7525","E7526","E7529","E754","F842","G10","G110",
"G111","G112","G113","G114","G118","G119","G120","G121",
"G1220","G1221","G1222","G1223","G1224","G1225","G1229",
"G128","G129","G132","G138","G20","G214","G2401","G2402",
"G2409","G242","G248","G254","G255","G2581","G300","G301",
"G308","G309","G3101","G3109","G311","G312","G3181","G3182",
"G3183","G3184","G3185","G3189","G319","G3281","G35","G361",
"G368","G369","G370","G371","G372","G373","G374","G375","G378",
"G379","G40001","G40009","G40011","G40019","G40101","G40109",
"G40111","G40119","G40201","G40209","G40211","G40219","G40301",
"G40309","G40311","G40319","G40401","G40409","G40411","G40419",
"G40501","G40509","G40801","G40802","G40803","G40804","G40811",
"G40812","G40813","G40814","G40821","G40822","G40823","G40824",
"G4089","G40901","G40909","G40911","G40919","G40A01","G40A09",
"G40A11","G40A19","G40B01","G40B09","G40B11","G40B19","G47411",
"G47419","G47421","G47429","G803","G890","G910","G911","G912",
"G913","G914","G918","G919","G937","G9389","G939","G94","O99350",
"O99351","O99352","O99353","O99354","O99355","P9160","P9161",
"P9162","P9163","R410","R4182","R4701","R5600","R5601","R561","R569")
chronic_pulm10beta <- c("J40","J410","J411","J418","J42","J430","J431",
"J432","J438","J439","J440","J441","J449","J4520",
"J4521","J4522","J4530","J4531","J4532","J4540",
"J4541","J4542","J4550","J4551","J4552","J45901",
"J45902","J45909","J45990","J45991","J45998","J470",
"J471","J479","J60","J61","J620","J628","J630",
"J631","J632","J633","J634","J635","J636","J64",
"J660","J661","J662","J668","J670","J671","J672",
"J673","J674","J675","J676","J677","J678","J679","J684")
diab_uc10beta <- c("E0800","E0801","E0810","E0811","E089","E0900","E0901",
"E0910","E0911","E099","E1010","E1011","E109","E1100",
"E1101","E1110","E1111","E119","E1300","E1301","E1310",
"E1311","E139","O24011","O24012","O24013","O24019",
"O2402","O2403","O24111","O24112","O24113","O24119",
"O2412","O2413","O24311","O24312","O24313","O24319",
"O2432","O2433","O24811","O24812","O24813","O24819",
"O2482","O2483","O24911","O24912","O24913","O24919",
"O2492","O2493")
diab_c10beta <- c("E0821","E0822","E0829","E08311","E08319","E08321",
"E083211","E083212","E083213","E083219","E08329","E083291",
"E083292","E083293","E083299","E08331","E083311","E083312",
"E083313","E083319","E08339","E083391","E083392","E083393",
"E083399","E08341","E083411","E083412","E083413","E083419",
"E08349","E083491","E083492","E083493","E083499","E08351",
"E083511","E083512","E083513","E083519","E083521","E083522",
"E083523","E083529","E083531","E083532","E083533","E083539",
"E083541","E083542","E083543","E083549","E083551","E083552",
"E083553","E083559","E08359","E083591","E083592","E083593",
"E083599","E0836","E0837X1","E0837X2","E0837X3","E0837X9",
"E0839","E0840","E0841","E0842","E0843","E0844","E0849",
"E0851","E0852","E0859","E08610","E08618","E08620","E08621",
"E08622","E08628","E08630","E08638","E08641","E08649","E0865",
"E0869","E088","E0921","E0922","E0929","E09311","E09319",
"E09321","E093211","E093212","E093213","E093219","E09329",
"E093291","E093292","E093293","E093299","E09331","E093311",
"E093312","E093313","E093319","E09339","E093391","E093392",
"E093393","E093399","E09341","E093411","E093412","E093413",
"E093419","E09349","E093491","E093492","E093493","E093499",
"E09351","E093511","E093512","E093513","E093519","E093521",
"E093522","E093523","E093529","E093531","E093532","E093533",
"E093539","E093541","E093542","E093543","E093549","E093551",
"E093552","E093553","E093559","E09359","E093591","E093592",
"E093593","E093599","E0936","E0937X1","E0937X2","E0937X3",
"E0937X9","E0939","E0940","E0941","E0942","E0943","E0944",
"E0949","E0951","E0952","E0959","E09610","E09618","E09620",
"E09621","E09622","E09628","E09630","E09638","E09641","E09649",
"E0965","E0969","E098","E1021","E1022","E1029","E10311",
"E10319","E10321","E103211","E103212","E103213","E103219",
"E10329","E103291","E103292","E103293","E103299","E10331",
"E103311","E103312","E103313","E103319","E10339","E103391",
"E103392","E103393","E103399","E10341","E103411","E103412",
"E103413","E103419","E10349","E103491","E103492","E103493",
"E103499","E10351","E103511","E103512","E103513","E103519",
"E103521","E103522","E103523","E103529","E103531","E103532",
"E103533","E103539","E103541","E103542","E103543","E103549",
"E103551","E103552","E103553","E103559","E10359","E103591",
"E103592","E103593","E103599","E1036","E1037X1","E1037X2",
"E1037X3","E1037X9","E1039","E1040","E1041","E1042","E1043",
"E1044","E1049","E1051","E1052","E1059","E10610","E10618",
"E10620","E10621","E10622","E10628","E10630","E10638","E10641",
"E10649","E1065","E1069","E108","E1121","E1122","E1129",
"E11311","E11319","E11321","E113211","E113212","E113213",
"E113219","E11329","E113291","E113292","E113293","E113299",
"E11331","E113311","E113312","E113313","E113319","E11339",
"E113391","E113392","E113393","E113399","E11341","E113411",
"E113412","E113413","E113419","E11349","E113491","E113492",
"E113493","E113499","E11351","E113511","E113512","E113513",
"E113519","E113521","E113522","E113523","E113529","E113531",
"E113532","E113533","E113539","E113541","E113542","E113543",
"E113549","E113551","E113552","E113553","E113559","E11359",
"E113591","E113592","E113593","E113599","E1136","E1137X1",
"E1137X2","E1137X3","E1137X9","E1139","E1140","E1141","E1142",
"E1143","E1144","E1149","E1151","E1152","E1159","E11610",
"E11618","E11620","E11621","E11622","E11628","E11630",
"E11638","E11641","E11649","E1165","E1169","E118","E1321",
"E1322","E1329","E13311","E13319","E13321","E133211","E133212",
"E133213","E133219","E13329","E133291","E133292","E133293",
"E133299","E13331","E133311","E133312","E133313","E133319",
"E13339","E133391","E133392","E133393","E133399","E13341",
"E133411","E133412","E133413","E133419","E13349","E133491",
"E133492","E133493","E133499","E13351","E133511","E133512",
"E133513","E133519","E133521","E133522","E133523","E133529",
"E133531","E133532","E133533","E133539","E133541","E133542",
"E133543","E133549","E133551","E133552","E133553","E133559",
"E13359","E133591","E133592","E133593","E133599","E1336",
"E1337X1","E1337X2","E1337X3","E1337X9","E1339","E1340",
"E1341","E1342","E1343","E1344","E1349","E1351","E1352",
"E1359","E13610","E13618","E13620","E13621","E13622","E13628",
"E13630","E13638","E13641","E13649","E1365","E1369","E138","P702")
hypo10beta <- c("E000","E001","E002","E009","E018","E02","E030","E031","E032",
"E033","E038","E039","E890")
renal10beta <- c("N183","N184","N185","N186","N189","N19","Z4901","Z4902",
"Z4931","Z4932","Z9115","Z940","Z992",
"I120") #hrnwrf
liver10beta <- c("B180","B181","B182","I8500","I8501","I8510","I8511",
"K700","K702","K7030","K7031","K7040","K7041","K709","
K7210","K7211","K7290","K7291","K730","K731","K732",
"K738","K739","K740","K741","K742","K743","K744","K745",
"K7460","K7469","K754","K7581","K760","K766","K7689","K769",
"Z944")
peptic10beta <- c("K254","K255","K256","K257","K259","K264","K265","K266",
"K267","K269","K274","K275","K276","K277","K279","K284",
"K285","K286","K287","K289")
hiv10beta <- c("B20")
lymph10beta <- c("C8100","C8101","C8102","C8103","C8104","C8105","C8106",
"C8107","C8108","C8109","C8110","C8111","C8112","C8113",
"C8114","C8115","C8116","C8117","C8118","C8119","C8120",
"C8121","C8122","C8123","C8124","C8125","C8126","C8127",
"C8128","C8129","C8130","C8131","C8132","C8133","C8134",
"C8135","C8136","C8137","C8138","C8139","C8140","C8141",
"C8142","C8143","C8144","C8145","C8146","C8147","C8148",
"C8149","C8170","C8171","C8172","C8173","C8174","C8175",
"C8176","C8177","C8178","C8179","C8190","C8191","C8192",
"C8193","C8194","C8195","C8196","C8197","C8198","C8199",
"C8200","C8201","C8202","C8203","C8204","C8205","C8206",
"C8207","C8208","C8209","C8210","C8211","C8212","C8213",
"C8214","C8215","C8216","C8217","C8218","C8219","C8220",
"C8221","C8222","C8223","C8224","C8225","C8226","C8227",
"C8228","C8229","C8230","C8231","C8232","C8233","C8234",
"C8235","C8236","C8237","C8238","C8239","C8240","C8241",
"C8242","C8243","C8244","C8245","C8246","C8247","C8248",
"C8249","C8250","C8251","C8252","C8253","C8254","C8255",
"C8256","C8257","C8258","C8259","C8260","C8261","C8262",
"C8263","C8264","C8265","C8266","C8267","C8268","C8269",
"C8280","C8281","C8282","C8283","C8284","C8285","C8286",
"C8287","C8288","C8289","C8290","C8291","C8292","C8293",
"C8294","C8295","C8296","C8297","C8298","C8299","C8300",
"C8301","C8302","C8303","C8304","C8305","C8306","C8307",
"C8308","C8309","C8310","C8311","C8312","C8313","C8314",
"C8315","C8316","C8317","C8318","C8319","C8330","C8331",
"C8332","C8333","C8334","C8335","C8336","C8337","C8338",
"C8339","C8350","C8351","C8352","C8353","C8354","C8355",
"C8356","C8357","C8358","C8359","C8370","C8371","C8372",
"C8373","C8374","C8375","C8376","C8377","C8378","C8379",
"C8380","C8381","C8382","C8383","C8384","C8385","C8386",
"C8387","C8388","C8389","C8390","C8391","C8392","C8393",
"C8394","C8395","C8396","C8397","C8398","C8399","C8400",
"C8401","C8402","C8403","C8404","C8405","C8406","C8407",
"C8408","C8409","C8410","C8411","C8412","C8413","C8414",
"C8415","C8416","C8417","C8418","C8419","C8440","C8441",
"C8442","C8443","C8444","C8445","C8446","C8447","C8448",
"C8449","C8460","C8461","C8462","C8463","C8464","C8465",
"C8466","C8467","C8468","C8469","C8470","C8471","C8472",
"C8473","C8474","C8475","C8476","C8477","C8478","C8479",
"C8490","C8491","C8492","C8493","C8494","C8495","C8496",
"C8497","C8498","C8499","C84A0","C84A1","C84A2","C84A3",
"C84A4","C84A5","C84A6","C84A7","C84A8","C84A9","C84Z0",
"C84Z1","C84Z2","C84Z3","C84Z4","C84Z5","C84Z6","C84Z7",
"C84Z8","C84Z9","C8510","C8511","C8512","C8513","C8514",
"C8515","C8516","C8517","C8518","C8519","C8520","C8521",
"C8522","C8523","C8524","C8525","C8526","C8527","C8528",
"C8529","C8580","C8581","C8582","C8583","C8584","C8585",
"C8586","C8587","C8588","C8589","C8590","C8591","C8592",
"C8593","C8594","C8595","C8596","C8597","C8598","C8599",
"C860","C861","C862","C863","C864","C865","C866","C880",
"C882","C883","C884","C888","C889","C9000","C9001","C9002",
"C9010","C9011","C9012","C9020","C9021","C9022","C9030",
"C9031","C9032","C960","C962","C9620","C9621","C9622",
"C9629","C964","C969","C96A","C96Z","D47Z9")
mets10beta <- c("C770","C771","C772","C773","C774","C775","C778","C779",
"C7800","C7801","C7802","C781","C782","C7830","C7839","C784",
"C785","C786","C787","C7880","C7889","C7900","C7901","C7902",
"C7910","C7911","C7919","C792","C7931","C7932","C7940","C7949",
"C7951","C7952","C7960","C7961","C7962","C7970","C7971","C7972",
"C7981","C7982","C7989","C799","C7B00","C7B01","C7B02","C7B03",
"C7B04","C7B09","C7B1","C7B8","C800","C801","R180")
tumor10beta <- c("C000","C001","C002","C003","C004","C005","C006","C008",
"C009","C01","C020","C021","C022","C023","C024","C028",
"C029","C030","C031","C039","C040","C041","C048","C049",
"C050","C051","C052","C058","C059","C060","C061","C062",
"C0680","C0689","C069","C07","C080","C081","C089","C090",
"C091","C098","C099","C100","C101","C102","C103","C104",
"C108","C109","C110","C111","C112","C113","C118","C119",
"C12","C130","C131","C132","C138","C139","C140","C142",
"C148","C153","C154","C155","C158","C159","C160","C161",
"C162","C163","C164","C165","C166","C168","C169","C170",
"C171","C172","C173","C178","C179","C180","C181","C182",
"C183","C184","C185","C186","C187","C188","C189","C19",
"C20","C210","C211","C212","C218","C220","C221","C222",
"C223","C224","C227","C228","C229","C23","C240","C241",
"C248","C249","C250","C251","C252","C253","C254","C257",
"C258","C259","C260","C261","C269","C300","C301","C310",
"C311","C312","C313","C318","C319","C320","C321","C322",
"C323","C328","C329","C33","C3400","C3401","C3402","C3410",
"C3411","C3412","C342","C3430","C3431","C3432","C3480",
"C3481","C3482","C3490","C3491","C3492","C37","C380","C381",
"C382","C383","C384","C388","C390","C399","C4000","C4001",
"C4002","C4010","C4011","C4012","C4020","C4021","C4022",
"C4030","C4031","C4032","C4080","C4081","C4082","C4090",
"C4091","C4092","C410","C411","C412","C413","C414","C419",
"C430","C4310","C4311","C43111","C43112","C4312","C43121",
"C43122","C4320","C4321","C4322","C4330","C4331","C4339",
"C434","C4351","C4352","C4359","C4360","C4361","C4362",
"C4370","C4371","C4372","C438","C439","C450","C451","C452",
"C457","C470","C4710","C4711","C4712","C4720","C4721","C4722",
"C473","C474","C475","C476","C478","C479","C480","C481","C482",
"C488","C490","C4910","C4911","C4912","C4920","C4921","C4922",
"C493","C494","C495","C496","C498","C499","C49A0","C49A1",
"C49A2","C49A3","C49A4","C49A5","C49A9","C4A0","C4A10",
"C4A11","C4A111","C4A112","C4A12","C4A121","C4A122",
"C4A20","C4A21","C4A22","C4A30","C4A31","C4A39","C4A4",
"C4A51","C4A52","C4A59","C4A60","C4A61","C4A62","C4A70",
"C4A71","C4A72","C4A8","C4A9","C50011","C50012","C50019",
"C50021","C50022","C50029","C50111","C50112","C50119",
"C50121","C50122","C50129","C50211","C50212","C50219",
"C50221","C50222","C50229","C50311","C50312","C50319",
"C50321","C50322","C50329","C50411","C50412","C50419",
"C50421","C50422","C50429","C50511","C50512","C50519",
"C50521","C50522","C50529","C50611","C50612","C50619",
"C50621","C50622","C50629","C50811","C50812","C50819",
"C50821","C50822","C50829","C50911","C50912","C50919",
"C50921","C50922","C50929","C510","C511","C512","C518",
"C519","C52","C530","C531","C538","C539","C540","C541",
"C542","C543","C548","C549","C55","C561","C562","C569",
"C5700","C5701","C5702","C5710","C5711","C5712","C5720",
"C5721","C5722","C573","C574","C577","C578","C579","C58",
"C600","C601","C602","C608","C609","C61","C6200","C6201",
"C6202","C6210","C6211","C6212","C6290","C6291","C6292",
"C6300","C6301","C6302","C6310","C6311","C6312","C632",
"C637","C638","C639","C641","C642","C649","C651","C652",
"C659","C661","C662","C669","C670","C671","C672","C673",
"C674","C675","C676","C677","C678","C679","C680","C681",
"C688","C689","C6900","C6901","C6902","C6910","C6911",
"C6912","C6920","C6921","C6922","C6930","C6931","C6932",
"C6940","C6941","C6942","C6950","C6951","C6952","C6960",
"C6961","C6962","C6980","C6981","C6982","C6990","C6991",
"C6992","C700","C701","C709","C710","C711","C712","C713",
"C714","C715","C716","C717","C718","C719","C720","C721",
"C7220","C7221","C7222","C7230","C7231","C7232","C7240",
"C7241","C7242","C7250","C7259","C729","C73","C7400",
"C7401","C7402","C7410","C7411","C7412","C7490","C7491",
"C7492","C750","C751","C752","C753","C754","C755","C758",
"C759","C760","C761","C762","C763","C7640","C7641","C7642",
"C7650","C7651","C7652","C768","C7A00","C7A010","C7A011",
"C7A012","C7A019","C7A020","C7A021","C7A022","C7A023",
"C7A024","C7A025","C7A026","C7A029","C7A090","C7A091",
"C7A092","C7A093","C7A094","C7A095","C7A096","C7A098",
"D030","D0310","D0311","D03111","D03112","D0312",
"D03121","D03122","D0320","D0321","D0322","D0330",
"D0339","D034","D0351","D0352","D0359","D0360","D0361",
"D0362","D0370","D0371","D0372","D038","D039","E3121",
"E3122","E3123")
rheum10beta <- c("L900","L940","L941","L943","M0500","M05011","M05012",
"M05019","M05021","M05022","M05029","M05031","M05032",
"M05039","M05041","M05042","M05049","M05051","M05052",
"M05059","M05061","M05062","M05069","M05071","M05072",
"M05079","M0509","M0510","M05111","M05112","M05119",
"M05121","M05122","M05129","M05131","M05132","M05139",
"M05141","M05142","M05149","M05151","M05152","M05159",
"M05161","M05162","M05169","M05171","M05172","M05179",
"M0519","M0520","M05211","M05212","M05219","M05221",
"M05222","M05229","M05231","M05232","M05239","M05241",
"M05242","M05249","M05251","M05252","M05259","M05261",
"M05262","M05269","M05271","M05272","M05279","M0529",
"M0530","M05311","M05312","M05319","M05321","M05322",
"M05329","M05331","M05332","M05339","M05341","M05342",
"M05349","M05351","M05352","M05359","M05361","M05362",
"M05369","M05371","M05372","M05379","M0539","M0540",
"M05411","M05412","M05419","M05421","M05422","M05429",
"M05431","M05432","M05439","M05441","M05442","M05449",
"M05451","M05452","M05459","M05461","M05462","M05469",
"M05471","M05472","M05479","M0549","M0550","M05511",
"M05512","M05519","M05521","M05522","M05529","M05531",
"M05532","M05539","M05541","M05542","M05549","M05551",
"M05552","M05559","M05561","M05562","M05569","M05571",
"M05572","M05579","M0559","M0560","M05611","M05612",
"M05619","M05621","M05622","M05629","M05631","M05632",
"M05639","M05641","M05642","M05649","M05651","M05652",
"M05659","M05661","M05662","M05669","M05671","M05672",
"M05679","M0569","M0570","M05711","M05712","M05719",
"M05721","M05722","M05729","M05731","M05732","M05739",
"M05741","M05742","M05749","M05751","M05752","M05759",
"M05761","M05762","M05769","M05771","M05772","M05779",
"M0579","M0580","M05811","M05812","M05819","M05821",
"M05822","M05829","M05831","M05832","M05839","M05841",
"M05842","M05849","M05851","M05852","M05859","M05861",
"M05862","M05869","M05871","M05872","M05879","M0589",
"M059","M0600","M06011","M06012","M06019","M06021",
"M06022","M06029","M06031","M06032","M06039","M06041",
"M06042","M06049","M06051","M06052","M06059","M06061",
"M06062","M06069","M06071","M06072","M06079","M0608",
"M0609","M061","M0620","M06211","M06212","M06219",
"M06221","M06222","M06229","M06231","M06232","M06239",
"M06241","M06242","M06249","M06251","M06252","M06259",
"M06261","M06262","M06269","M06271","M06272","M06279",
"M0628","M0629","M0630","M06311","M06312","M06319",
"M06321","M06322","M06329","M06331","M06332","M06339",
"M06341","M06342","M06349","M06351","M06352","M06359",
"M06361","M06362","M06369","M06371","M06372","M06379",
"M0638","M0639","M064","M0680","M06811","M06812","M06819",
"M06821","M06822","M06829","M06831","M06832","M06839",
"M06841","M06842","M06849","M06851","M06852","M06859",
"M06861","M06862","M06869","M06871","M06872","M06879",
"M0688","M0689","M069","M0800","M08011","M08012","M08019",
"M08021","M08022","M08029","M08031","M08032","M08039",
"M08041","M08042","M08049","M08051","M08052","M08059",
"M08061","M08062","M08069","M08071","M08072","M08079",
"M0808","M0809","M081","M0820","M08211","M08212","M08219",
"M08221","M08222","M08229","M08231","M08232","M08239",
"M08241","M08242","M08249","M08251","M08252","M08259",
"M08261","M08262","M08269","M08271","M08272","M08279",
"M0828","M0829","M083","M0840","M08411","M08412","M08419",
"M08421","M08422","M08429","M08431","M08432","M08439",
"M08441","M08442","M08449","M08451","M08452","M08459",
"M08461","M08462","M08469","M08471","M08472","M08479",
"M0848","M0880","M08811","M08812","M08819","M08821",
"M08822","M08829","M08831","M08832","M08839","M08841",
"M08842","M08849","M08851","M08852","M08859","M08861",
"M08862","M08869","M08871","M08872","M08879","M0888",
"M0889","M0890","M08911","M08912","M08919","M08921",
"M08922","M08929","M08931","M08932","M08939","M08941",
"M08942","M08949","M08951","M08952","M08959","M08961",
"M08962","M08969","M08971","M08972","M08979","M0898",
"M0899","M1200","M12011","M12012","M12019","M12021",
"M12022","M12029","M12031","M12032","M12039","M12041",
"M12042","M12049","M12051","M12052","M12059","M12061",
"M12062","M12069","M12071","M12072","M12079","M1208",
"M1209","M320","M3210","M3211","M3212","M3213","M3214",
"M3215","M3219","M328","M329","M3300","M3301","M3302",
"M3303","M3309","M3310","M3311","M3312","M3313","M3319",
"M3320","M3321","M3322","M3329","M3390","M3391","M3392",
"M3393","M3399","M340","M341","M342","M3481","M3482","M3483",
"M3489","M349","M3500","M3501","M3502","M3503","M3504",
"M3509","M351","M353","M355","M358","M359","M360","M368",
"M450","M451","M452","M453","M454","M455","M456","M457",
"M458","M459","M4600","M4601","M4602","M4603","M4604",
"M4605","M4606","M4607","M4608","M4609","M461","M4650",
"M4651","M4652","M4653","M4654","M4655","M4656","M4657",
"M4658","M4659","M4680","M4681","M4682","M4683","M4684",
"M4685","M4686","M4687","M4688","M4689","M4690","M4691",
"M4692","M4693","M4694","M4695","M4696","M4697","M4698",
"M4699","M488X1","M488X2","M488X3","M488X4","M488X5",
"M488X6","M488X7","M488X8","M488X9","M4980","M4981",
"M4982","M4983","M4984","M4985","M4986","M4987","M4988",
"M4989")
coag10beta <- c("D65","D66","D67","D680","D681","D682","D68311","D68312",
"D68318","D6832","D684","D688","D689","D691","D693","D6941",
"D6942","D6949","D6951","D6959","D696","D7582","O99111",
"O99112","O99113","O99119","O9912","O9913")
obese10beta <- c("E6601","E6609","E661","E662","E668","E669","O99210",
"O99211","O99212","O99213","O99214","O99215","R939",
"Z6830","Z6831","Z6832","Z6833","Z6834","Z6835","Z6836",
"Z6837","Z6838","Z6839","Z6841","Z6842","Z6843","Z6844",
"Z6845","Z6854")
weightloss10beta <- c("E40","E41","E42","E43","E440","E441","E45","E46",
"E640","R634","R636")
fluid10beta <- c("E860","E861","E869","E870","E871","E872","E873","E874",
"E875","E876","E8770","E8771","E8779","E878")
bld_anem10beta <- c("D500","O9081","O99011","O99012","O99013","O99019",
"O9902","O9903")
def_anem10beta <- c("D501","D508","D509","D510","D511","D512","D513",
"D518","D519","D520","D521","D528","D529","D530",
"D531","D532","D538","D539","D630","D631","D638",
"D649")
alcohol10beta <- c("F1010","F1011","F10120","F10121","F10129","F1014",
"F10150","F10151","F10159","F10180","F10181","F10182",
"F10188","F1019","F1020","F1021","F10220","F10221",
"F10229","F10230","F10231","F10232","F10239","F1024",
"F10250","F10251","F10259","F1026","F1027","F10280",
"F10281","F10282","F10288","F1029","F10921","F1094",
"F10950","F10951","F10959","F1096","F1097","F10980",
"F10981","F10982","F10988","F1099")
drug10beta <- c("F1110","F1111","F11120","F11121","F11122","F11129",
"F1114","F11150","F11151","F11159","F11181","F11182",
"F11188","F1119","F1120","F1121","F11220","F11221",
"F11222","F11229","F1123","F1124","F11250","F11251",
"F11259","F11281","F11282","F11288","F1129","F1210",
"F1211","F12120","F12121","F12122","F12129","F12150",
"F12151","F12159","F12180","F12188","F1219","F1220",
"F1221","F12220","F12221","F12222","F12229","F1223",
"F12250","F12251","F12259","F12280","F12288","F1229",
"F1310","F1311","F13120","F13121","F13129","F1314",
"F13150","F13151","F13159","F13180","F13181","F13182",
"F13188","F1319","F1320","F1321","F13220","F13221",
"F13229","F13230","F13231","F13232","F13239","F1324",
"F13250","F13251","F13259","F1326","F1327","F13280",
"F13281","F13282","F13288","F1329","F1410","F1411",
"F14120","F14121","F14122","F14129","F1414","F14150",
"F14151","F14159","F14180","F14181","F14182","F14188",
"F1419","F1420","F1421","F14220","F14221","F14222",
"F14229","F1423","F1424","F14250","F14251","F14259",
"F14280","F14281","F14282","F14288","F1429","F1510",
"F1511","F15120","F15121","F15122","F15129","F1514",
"F15150","F15151","F15159","F15180","F15181","F15182",
"F15188","F1519","F1520","F1521","F15220","F15221",
"F15222","F15229","F1523","F1524","F15250","F15251",
"F15259","F15280","F15281","F15282","F15288","F1529",
"F1610","F1611","F16120","F16121","F16122","F16129",
"F1614","F16150","F16151","F16159","F16180","F16183",
"F16188","F1619","F1620","F1621","F16220","F16221",
"F16229","F1624","F16250","F16251","F16259","F16280",
"F16283","F16288","F1629","F1810","F1811","F18120",
"F18121","F18129","F1814","F18150","F18151","F18159",
"F1817","F18180","F18188","F1819","F1820","F1821",
"F18220","F18221","F18229","F1824","F18250","F18251",
"F18259","F1827","F18280","F18288","F1829","F1910",
"F1911","F19120","F19121","F19122","F19129","F1914",
"F19150","F19151","F19159","F1916","F1917","F19180",
"F19181","F19182","F19188","F1919","F1920","F1921","F19220",
"F19221","F19222","F19229","F19230","F19231","F19232",
"F19239","F1924","F19250","F19251","F19259","F1926","F1927",
"F19280","F19281","F19282","F19288","F1929","F550","F551",
"F552","F553","F554","F558","O99320","O99321","O99322",
"O99323","O99324","O99325")
psych10beta <- c("F200","F201","F202","F203","F205","F2081","F2089","F209",
"F22","F23","F24","F250","F251","F258","F259","F28","F29",
"F3010","F3011","F3012","F3013","F302","F303","F304","F308",
"F309","F310","F3110","F3111","F3112","F3113","F312","F3130",
"F3131","F3132","F314","F315","F3160","F3161","F3162","F3163",
"F3164","F3170","F3171","F3172","F3173","F3174","F3175",
"F3176","F3177","F3178","F3181","F3189","F319","F324",
"F325","F3340","F3341","F3342","F348","F3481","F3489",
"F349","F39","F4489","F843")
depress10beta <- c("F320","F321","F322","F323","F328","F3281","F3289",
"F329","F330","F331","F332","F333","F338","F339",
"F341","F4321")
# Code -----
dat <- dat %>%
dplyr::filter({{version_var}} == 9 | {{version_var}} == 10)
dat1 <- dat %>%
dplyr::mutate(chf = dplyr::if_else(({{version_var}} == 9 & (dx %in% chf9 )| stringr::str_starts(dx, paste(chf9_str))) |
({{version_var}} == 10 & (dx %in% chf10beta)),
1, 0),
valve = dplyr::if_else(({{version_var}} == 9 & (dx %in% valve9 | stringr::str_starts(dx, paste(valve9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% valve10beta),
1, 0),
pulmcirc = dplyr::if_else(({{version_var}} == 9 & (dx %in% pulmcirc9 | stringr::str_starts(dx, paste(pulmcirc9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% pulmcirc10beta),
1, 0),
periph_vasc = dplyr::if_else(({{version_var}} == 9 & (dx %in% periph_vasc9 | stringr::str_starts(dx, paste(periph_vasc9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% periph_vasc10beta),
1, 0),
htn_uc = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(htn_uc9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% htn_uc10beta),
1, 0),
htn_c = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(htn_c9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% htn_c10beta),
1 ,0),
paralysis = dplyr::if_else(({{version_var}} == 9 & (dx %in% paralysis9 | stringr::str_starts(dx, paste(paralysis9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% paralysis10beta),
1, 0),
neuro = dplyr::if_else(({{version_var}} == 9 & (dx %in% neuro9 | stringr::str_starts(dx, paste(neuro9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% neuro10beta),
1, 0),
chronic_pulm = dplyr::if_else(({{version_var}} == 9 & (dx %in% chronic_pulm9 | stringr::str_starts(dx, paste(chronic_pulm9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% chronic_pulm10beta),
1, 0),
diab_uc = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(diab_uc9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% diab_uc10beta),
1, 0),
diab_c = dplyr::if_else(({{version_var}} == 9 & (dx %in% diab_c9 | stringr::str_starts(dx, paste(diab_c9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% diab_c10beta),
1, 0),
hypo = dplyr::if_else(({{version_var}} == 9 & dx %in% hypo9) |
({{version_var}} == 10 & dx %in% hypo10beta),
1, 0),
renal = dplyr::if_else(({{version_var}} == 9 & (dx %in% renal9 | stringr::str_starts(dx, paste(renal9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% renal10beta),
1, 0),
liver = dplyr::if_else(({{version_var}} == 9 & (dx %in% liver9 | stringr::str_starts(dx, paste(liver9_str)))) |
({{version_var}} == 10 & dx %in% liver10beta),
1, 0),
peptic = dplyr::if_else(({{version_var}} == 9 & dx %in% peptic9) |
({{version_var}} == 10 & dx %in% peptic10beta),
1, 0),
hiv = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(hiv9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% hiv10beta),
1 ,0),
lymph = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(lymph9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% lymph10beta),
1, 0),
mets = dplyr::if_else(({{version_var}} == 9 & (dx %in% mets9 | stringr::str_starts(dx, paste(mets9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% mets10beta),
1, 0),
tumor = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(tumor9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% tumor10beta),
1, 0),
rheum = dplyr::if_else(({{version_var}} == 9 & (dx %in% rheum9 | stringr::str_starts(dx, paste(rheum9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% rheum10beta),
1, 0),
coag = dplyr::if_else(({{version_var}} == 9 & (dx %in% coag9 | stringr::str_starts(dx, paste(coag9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% coag10beta),
1, 0),
obese = dplyr::if_else(({{version_var}} == 9 & (dx %in% obese9 | stringr::str_starts(dx, paste(obese9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% obese10beta),
1, 0),
weightloss = dplyr::if_else(({{version_var}} == 9 & (dx %in% weightloss9 | stringr::str_starts(dx, paste(weightloss9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% weightloss10beta),
1, 0),
fluid = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(fluid9_str))) |
({{version_var}} == 10 & dx %in% fluid10beta),
1, 0),
bld_anem = dplyr::if_else(({{version_var}} == 9 & (dx %in% bld_anem9 | stringr::str_starts(dx, paste(bld_anem9_str)))) |
({{version_var}} == 10 & dx %in% bld_anem10beta),
1, 0),
def_anem = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(def_anem9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% def_anem10beta),
1, 0),
alcohol = dplyr::if_else(({{version_var}} == 9 & (dx %in% alc9 | stringr::str_starts(dx, paste(alcohol9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% alcohol10beta),
1, 0),
drug = dplyr::if_else(({{version_var}} == 9 & (dx %in% drug9 | stringr::str_starts(dx, paste(drug9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% drug10beta),
1, 0),
psych = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(psych9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% psych10beta),
1, 0),
depression = dplyr::if_else(({{version_var}} == 9 & dx %in% depress9) |
({{version_var}} == 10 & dx %in% depress10beta),
1, 0))
dat1 <- dat1 %>%
dplyr::mutate(htn_uc = dplyr::if_else(.data$htn_c == 1, 0,.data$htn_uc),
tumor = dplyr::if_else(.data$mets == 1, 0, .data$tumor),
diab_uc = dplyr::if_else(.data$diab_c == 1, 0, .data$diab_uc),
htn_comb = dplyr::if_else(.data$htn_c == 1 | .data$htn_uc == 1, 1, 0))
}
else {stop("Please specify the version (9 = ICD9, 10 = ICD10, or 19 = ICD9 and ICD10) of your diagnoses codes.")
}
# Outpatient Algorithms ----
## No OT Limitation ----
### ICD-9 or Both ----
if (outpatient_two == "no" & (version == 9 | version == 19)){
dat2 <- dplyr::rename(dat1, "id" = id2)
dat2 <- dat2 %>%
dplyr::mutate(elix_chf = .data$chf,
elix_valve = .data$valve,
elix_pulmcirc = .data$pulmcirc,
elix_periph_vasc = .data$periph_vasc,
elix_htn_uc = .data$htn_uc,
elix_htn_c = .data$htn_c,
elix_paralysis = .data$paralysis,
elix_neuro = .data$neuro,
elix_chronic_pulm = .data$chronic_pulm,
elix_diab_uc = .data$diab_uc,
elix_diab_c = .data$diab_c,
elix_hypo = .data$hypo,
elix_renal = .data$renal,
elix_liver = .data$liver,
elix_peptic = .data$peptic,
elix_hiv = .data$hiv,
elix_lymph = .data$lymph,
elix_mets = .data$mets,
elix_tumor = .data$tumor,
elix_rheum = .data$rheum,
elix_coag = .data$coag,
elix_obese = .data$obese,
elix_weightloss = .data$weightloss,
elix_fluid = .data$fluid,
elix_bld_anem = .data$bld_anem,
elix_def_anem = .data$def_anem,
elix_alcohol = .data$alcohol,
elix_drug = .data$drug,
elix_psych = .data$psych,
elix_depression = .data$depression)
dat2 <- dat2 %>%
dplyr::select(id, tidyselect::starts_with("elix"))
}
### ICD_10 ----
else if (outpatient_two == "no" & version == 10){
dat2 <- dplyr::rename(dat1, "id" = id2)
dat2 <- dat2 %>%
dplyr::mutate(elix_aids = .data$aids,
elix_alcohol = .data$alcohol,
elix_def_anem = .data$def_anem,
elix_rheum = .data$rheum,
elix_bld_loss = .data$bld_loss,
elix_cancer_leuk = .data$cancer_leuk,
elix_cancer_lymph = .data$cancer_lymph,
elix_cancer_mets = .data$cancer_mets,
elix_cancer_solid = .data$cancer_solid,
elix_cancer_insitu = .data$cancer_insitu,
elix_cbvd = .data$cbvd,
elix_chf = .data$chf,
elix_coag = .data$coag,
elix_dementia = .data$dementia,
elix_depress = .data$depress,
elix_diab_c = .data$diab_c,
elix_diab_uc = .data$diab_uc,
elix_drug = .data$drug,
elix_htn_c = .data$htn_c,
elix_htn_uc = .data$htn_uc,
elix_liver_mild = .data$liver_mild,
elix_liver_sev = .data$liver_sev,
elix_chronic_pulm = .data$chronic_pulm,
elix_neuro_movt = .data$neuro_movt,
elix_neuro_seiz = .data$neuro_seiz,
elix_neuro_oth = .data$neuro_oth,
elix_obese = .data$obese,
elix_paralysis = .data$paralysis,
elix_perivasc = .data$perivasc,
elix_psych = .data$psych,
elix_pulmcirc = .data$pulmcirc,
elix_renal_mod = .data$renal_mod,
elix_renal_sev = .data$renal_sev,
elix_hypo = .data$hypo,
elix_thyroid_oth = .data$thyroid_oth,
elix_peptic = .data$peptic,
elix_valve = .data$valve,
elix_weightloss = .data$weightloss)
dat2 <- dat2 %>%
dplyr::select(id, tidyselect::starts_with("elix"))
}
## ICD-9 or Both ----
else if ((outpatient_two == "yes" | outpatient_two == "Yes") & (version == 9 | version == 19)){
message("Message: You have specified that for a comorbidity to be positvely coded, an individual must have two outpatient claims with it. Please make sure the levels of your variable denoting outpatient type are either 'ot' or 'OT'")
dat_ot <- dat1 %>%
dplyr::filter(.data$type == "ot" | .data$type == "OT")
dat_ip <- dat1 %>%
dplyr::filter(.data$type != "ot" & .data$type != "OT")
dat_ot_sum <- dat_ot %>%
dplyr::group_by({{id}}) %>%
dplyr::summarize(
chf_ot = sum(.data$chf),
valve_ot = sum(.data$valve),
pulmcirc_ot = sum(.data$pulmcirc),
periph_vasc_ot = sum(.data$periph_vasc),
htn_uc_ot = sum(.data$htn_uc),
htn_c_ot = sum(.data$htn_c),
paralysis_ot = sum(.data$paralysis),
neuro_ot = sum(.data$neuro),
chronic_pulm_ot = sum(.data$chronic_pulm),
diab_uc_ot = sum(.data$diab_uc),
diab_c_ot = sum(.data$diab_c),
hypo_ot = sum(.data$hypo),
renal_ot = sum(.data$renal),
liver_ot = sum(.data$liver),
peptic_ot = sum(.data$peptic),
hiv_ot = sum(.data$hiv),
lymph_ot = sum(.data$lymph),
mets_ot = sum(.data$mets),
tumor_ot = sum(.data$tumor),
rheum_ot = sum(.data$rheum),
coag_ot = sum(.data$coag),
obese_ot = sum(.data$obese),
weightloss_ot = sum(.data$weightloss),
fluid_ot = sum(.data$fluid),
bld_anem_ot = sum(.data$bld_anem),
def_anem_ot = sum(.data$def_anem),
alcohol_ot = sum(.data$alcohol),
drug_ot = sum(.data$drug),
psych_ot = sum(.data$psych),
depression_ot = sum(.data$depression)) %>%
dplyr::ungroup()
dat_ip_sum <- dat_ip %>%
dplyr::group_by({{id}}) %>%
dplyr::summarize(
chf_ip = max(.data$chf),
valve_ip = max(.data$valve),
pulmcirc_ip = max(.data$pulmcirc),
periph_vasc_ip = max(.data$periph_vasc),
htn_uc_ip = max(.data$htn_uc),
htn_c_ip = max(.data$htn_c),
paralysis_ip = max(.data$paralysis),
neuro_ip = max(.data$neuro),
chronic_pulm_ip = max(.data$chronic_pulm),
diab_uc_ip = max(.data$diab_uc),
diab_c_ip = max(.data$diab_c),
hypo_ip = max(.data$hypo),
renal_ip = max(.data$renal),
liver_ip = max(.data$liver),
peptic_ip = max(.data$peptic),
hiv_ip = max(.data$hiv),
lymph_ip = max(.data$lymph),
mets_ip = max(.data$mets),
tumor_ip = max(.data$tumor),
rheum_ip = max(.data$rheum),
coag_ip = max(.data$coag),
obese_ip = max(.data$obese),
weightloss_ip = max(.data$weightloss),
fluid_ip = max(.data$fluid),
bld_anem_ip = max(.data$bld_anem),
def_anem_ip = max(.data$def_anem),
alcohol_ip = max(.data$alcohol),
drug_ip = max(.data$drug),
psych_ip = max(.data$psych),
depression_ip = max(.data$depression)) %>%
dplyr::ungroup()
dat_ip_sum <- dplyr::rename(dat_ip_sum, "id" = id2)
dat_ot_sum <- dplyr::rename(dat_ot_sum, "id" = id2)
dat_comb <- dplyr::full_join(dat_ip_sum, dat_ot_sum, by = "id")
dat_comb <- dat_comb %>%
dplyr::mutate(elix_chf = dplyr::if_else(.data$chf_ot >= 2 | .data$chf_ip >=1, 1, 0, missing = 0),
elix_valve = dplyr::if_else(.data$valve_ot >= 2 | .data$valve_ip >=1, 1, 0, missing = 0),
elix_pulmcirc = dplyr::if_else(.data$pulmcirc_ot >= 2 | .data$pulmcirc_ip >=1, 1, 0, missing = 0),
elix_periph_vasc = dplyr::if_else(.data$periph_vasc_ot >= 2 | .data$periph_vasc_ip >=1, 1, 0, missing = 0),
elix_htn_uc = dplyr::if_else(.data$htn_uc_ot >= 2 | .data$htn_uc_ip >=1, 1, 0, missing = 0),
elix_htn_c = dplyr::if_else(.data$htn_c_ot >= 2 | .data$htn_c_ip >=1, 1, 0, missing = 0),
elix_paralysis = dplyr::if_else(.data$paralysis_ot >= 2 | .data$paralysis_ip >=1, 1, 0, missing = 0),
elix_neuro = dplyr::if_else(.data$neuro_ot >= 2 | .data$neuro_ip >=1, 1, 0, missing = 0),
elix_chronic_pulm = dplyr::if_else(.data$chronic_pulm_ot >= 2 | .data$chronic_pulm_ip >=1, 1, 0, missing = 0),
elix_diab_uc = dplyr::if_else(.data$diab_uc_ot >= 2 | .data$diab_uc_ip >=1, 1, 0, missing = 0),
elix_diab_c = dplyr::if_else(.data$diab_c_ot >= 2 | .data$diab_c_ip >=1, 1, 0, missing = 0),
elix_hypo = dplyr::if_else(.data$hypo_ot >= 2 | .data$hypo_ip >=1, 1, 0, missing = 0),
elix_renal = dplyr::if_else(.data$renal_ot >= 2 | .data$renal_ip >=1, 1, 0, missing = 0),
elix_liver = dplyr::if_else(.data$liver_ot >= 2 | .data$liver_ip >=1, 1, 0, missing = 0),
elix_peptic = dplyr::if_else(.data$peptic_ot >= 2 | .data$peptic_ip >=1, 1, 0, missing = 0),
elix_hiv = dplyr::if_else(.data$hiv_ot >= 2 | .data$hiv_ip >=1, 1, 0, missing = 0),
elix_lymph = dplyr::if_else(.data$lymph_ot >= 2 | .data$lymph_ip >=1, 1, 0, missing = 0),
elix_mets = dplyr::if_else(.data$mets_ot >= 2 | .data$mets_ip >=1, 1, 0, missing = 0),
elix_tumor = dplyr::if_else(.data$tumor_ot >= 2 | .data$tumor_ip >=1, 1, 0, missing = 0),
elix_rheum = dplyr::if_else(.data$rheum_ot >= 2 | .data$rheum_ip >=1, 1, 0, missing = 0),
elix_coag = dplyr::if_else(.data$coag_ot >= 2 | .data$coag_ip >=1, 1, 0, missing = 0),
elix_obese = dplyr::if_else(.data$obese_ot >= 2 | .data$obese_ip >=1, 1, 0, missing = 0),
elix_weightloss = dplyr::if_else(.data$weightloss_ot >= 2 | .data$weightloss_ip >=1, 1, 0, missing = 0),
elix_fluid = dplyr::if_else(.data$fluid_ot >= 2 | .data$fluid_ip >=1, 1, 0, missing = 0),
elix_bld_anem = dplyr::if_else(.data$bld_anem_ot >= 2 | .data$bld_anem_ip >=1, 1, 0, missing = 0),
elix_def_anem = dplyr::if_else(.data$def_anem_ot >= 2 | .data$def_anem_ip >=1, 1, 0, missing = 0),
elix_alcohol = dplyr::if_else(.data$alcohol_ot >= 2 | .data$alcohol_ip >=1, 1, 0, missing = 0),
elix_drug = dplyr::if_else(.data$drug_ot >= 2 | .data$drug_ip >=1, 1, 0, missing = 0),
elix_psych = dplyr::if_else(.data$psych_ot >= 2 | .data$psych_ip >=1, 1, 0, missing = 0),
elix_depression = dplyr::if_else(.data$depression_ot >= 2 | .data$depression_ip >=1, 1, 0, missing = 0))
dat2 <- dat_comb %>%
dplyr::select(id, tidyselect::starts_with("elix"))
}
## ICD-10 ----
else if(outpatient_two == "yes" | outpatient_two == "Yes"){
message("Message: You have specified that for a comorbidity to be positvely coded, an individual must have two outpatient claims with it. Please make sure the levels of your variable denoting outpatient type must be either 'ot' or 'OT'")
dat_ot <- dat1 %>%
dplyr::filter(.data$type == "ot" | .data$type == "OT")
dat_ip <- dat1 %>%
dplyr::filter(.data$type != "ot" & .data$type != "OT")
dat_ot_sum <- dat_ot %>%
dplyr::group_by({{id}}) %>%
dplyr::summarize(
aids_ot = sum(.data$aids),
alcohol_ot = sum(.data$alcohol),
def_anem_ot = sum(.data$def_anem),
rheum_ot = sum(.data$rheum),
bld_loss_ot = sum(.data$bld_loss),
cancer_leuk_ot = sum(.data$cancer_leuk),
cancer_lymph_ot = sum(.data$cancer_lymph),
cancer_mets_ot = sum(.data$cancer_mets),
cancer_solid_ot = sum(.data$cancer_solid),
cancer_insitu_ot = sum(.data$cancer_insitu),
cbvd_ot = sum(.data$cbvd),
chf_ot = sum(.data$chf),
coag_ot = sum(.data$coag),
dementia_ot = sum(.data$dementia),
depress_ot = sum(.data$depress),
diab_c_ot = sum(.data$diab_c),
diab_uc_ot = sum(.data$diab_uc),
drug_ot = sum(.data$drug),
htn_c_ot = sum(.data$htn_c),
htn_uc_ot = sum(.data$htn_uc),
liver_mild_ot = sum(.data$liver_mild),
liver_sev_ot = sum(.data$liver_sev),
chronic_pulm_ot = sum(.data$chronic_pulm),
neuro_movt_ot = sum(.data$neuro_movt),
neuro_seiz_ot = sum(.data$neuro_seiz),
neuro_oth_ot = sum(.data$neuro_oth),
obese_ot = sum(.data$obese),
paralysis_ot = sum(.data$paralysis),
perivasc_ot = sum(.data$perivasc),
psych_ot = sum(.data$psych),
pulmcirc_ot = sum(.data$pulmcirc),
renal_mod_ot = sum(.data$renal_mod),
renal_sev_ot = sum(.data$renal_sev),
hypo_ot = sum(.data$hypo),
thyroid_oth_ot = sum(.data$thyroid_oth),
peptic_ot = sum(.data$peptic),
valve_ot = sum(.data$valve),
weightloss_ot = sum(.data$weightloss)) %>%
dplyr::ungroup()
dat_ip_sum <- dat_ip %>%
dplyr::group_by({{id}}) %>%
dplyr::summarize(
aids_ip = max(.data$aids),
alcohol_ip = max(.data$alcohol),
def_anem_ip = max(.data$def_anem),
rheum_ip = max(.data$rheum),
bld_loss_ip = max(.data$bld_loss),
cancer_leuk_ip = max(.data$cancer_leuk),
cancer_lymph_ip = max(.data$cancer_lymph),
cancer_mets_ip = max(.data$cancer_mets),
cancer_solid_ip = max(.data$cancer_solid),
cancer_insitu_ip = max(.data$cancer_insitu),
cbvd_ip = max(.data$cbvd),
chf_ip = max(.data$chf),
coag_ip = max(.data$coag),
dementia_ip = max(.data$dementia),
depress_ip = max(.data$depress),
diab_c_ip = max(.data$diab_c),
diab_uc_ip = max(.data$diab_uc),
drug_ip = max(.data$drug),
htn_c_ip = max(.data$htn_c),
htn_uc_ip = max(.data$htn_uc),
liver_mild_ip = max(.data$liver_mild),
liver_sev_ip = max(.data$liver_sev),
chronic_pulm_ip = max(.data$chronic_pulm),
neuro_movt_ip = max(.data$neuro_movt),
neuro_seiz_ip = max(.data$neuro_seiz),
neuro_oth_ip = max(.data$neuro_oth),
obese_ip = max(.data$obese),
paralysis_ip = max(.data$paralysis),
perivasc_ip = max(.data$perivasc),
psych_ip = max(.data$psych),
pulmcirc_ip = max(.data$pulmcirc),
renal_mod_ip = max(.data$renal_mod),
renal_sev_ip = max(.data$renal_sev),
hypo_ip = max(.data$hypo),
thyroid_oth_ip = max(.data$thyroid_oth),
peptic_ip = max(.data$peptic),
valve_ip = max(.data$valve),
weightloss_ip = max(.data$weightloss)) %>%
dplyr::ungroup()
dat_ip_sum <- dplyr::rename(dat_ip_sum, "id" = id2)
dat_ot_sum <- dplyr::rename(dat_ot_sum, "id" = id2)
dat_comb <- dplyr::full_join(dat_ip_sum, dat_ot_sum, by = "id")
dat_comb <- dat_comb %>%
dplyr::mutate(elix_aids = dplyr::if_else(.data$aids_ot >= 2 | .data$aids_ip >= 1, 1, 0, missing = 0),
elix_alcohol = dplyr::if_else(.data$alcohol_ot >= 2 | .data$alcohol_ip >= 1, 1, 0, missing = 0),
elix_def_anem = dplyr::if_else(.data$def_anem_ot >= 2 | .data$def_anem_ip >= 1, 1, 0, missing = 0),
elix_rheum = dplyr::if_else(.data$rheum_ot >= 2 | .data$rheum_ip >= 1, 1, 0, missing = 0),
elix_bld_loss = dplyr::if_else(.data$bld_loss_ot >= 2 | .data$bld_loss_ip >= 1, 1, 0, missing = 0),
elix_cancer_leuk = dplyr::if_else(.data$cancer_leuk_ot >= 2 | .data$cancer_leuk_ip >= 1, 1, 0, missing = 0),
elix_cancer_lymph = dplyr::if_else(.data$cancer_lymph_ot >= 2 | .data$cancer_lymph_ip >= 1, 1, 0, missing = 0),
elix_cancer_mets = dplyr::if_else(.data$cancer_mets_ot >= 2 | .data$cancer_mets_ip >= 1, 1, 0, missing = 0),
elix_cancer_solid = dplyr::if_else(.data$cancer_solid_ot >= 2 | .data$cancer_solid_ip >= 1, 1, 0, missing = 0),
elix_cancer_insitu = dplyr::if_else(.data$cancer_insitu_ot >= 2 | .data$cancer_insitu_ip >= 1, 1, 0, missing = 0),
elix_cbvd = dplyr::if_else(.data$cbvd_ot >= 2 | .data$cbvd_ip >= 1, 1, 0, missing = 0),
elix_chf = dplyr::if_else(.data$chf_ot >= 2 | .data$chf_ip >= 1, 1, 0, missing = 0),
elix_coag = dplyr::if_else(.data$coag_ot >= 2 | .data$coag_ip >= 1, 1, 0, missing = 0),
elix_dementia = dplyr::if_else(.data$dementia_ot >= 2 | .data$dementia_ip >= 1, 1, 0, missing = 0),
elix_depress = dplyr::if_else(.data$depress_ot >= 2 | .data$depress_ip >= 1, 1, 0, missing = 0),
elix_diab_c = dplyr::if_else(.data$diab_c_ot >= 2 | .data$diab_c_ip >= 1, 1, 0, missing = 0),
elix_diab_uc = dplyr::if_else(.data$diab_uc_ot >= 2 | .data$diab_uc_ip >= 1, 1, 0, missing = 0),
elix_drug = dplyr::if_else(.data$drug_ot >= 2 | .data$drug_ip >= 1, 1, 0, missing = 0),
elix_htn_c = dplyr::if_else(.data$htn_c_ot >= 2 | .data$htn_c_ip >= 1, 1, 0, missing = 0),
elix_htn_uc = dplyr::if_else(.data$htn_uc_ot >= 2 | .data$htn_uc_ip >= 1, 1, 0, missing = 0),
elix_liver_mild = dplyr::if_else(.data$liver_mild_ot >= 2 | .data$liver_mild_ip >= 1, 1, 0, missing = 0),
elix_liver_sev = dplyr::if_else(.data$liver_sev_ot >= 2 | .data$liver_sev_ip >= 1, 1, 0, missing = 0),
elix_chronic_pulm = dplyr::if_else(.data$chronic_pulm_ot >= 2 | .data$chronic_pulm_ip >= 1, 1, 0, missing = 0),
elix_neuro_movt = dplyr::if_else(.data$neuro_movt_ot >= 2 | .data$neuro_movt_ip >= 1, 1, 0, missing = 0),
elix_neuro_seiz = dplyr::if_else(.data$neuro_seiz_ot >= 2 | .data$neuro_seiz_ip >= 1, 1, 0, missing = 0),
elix_neuro_oth = dplyr::if_else(.data$neuro_oth_ot >= 2 | .data$neuro_oth_ip >= 1, 1, 0, missing = 0),
elix_obese = dplyr::if_else(.data$obese_ot >= 2 | .data$obese_ip >= 1, 1, 0, missing = 0),
elix_paralysis = dplyr::if_else(.data$paralysis_ot >= 2 | .data$paralysis_ip >= 1, 1, 0, missing = 0),
elix_perivasc = dplyr::if_else(.data$perivasc_ot >= 2 | .data$perivasc_ip >= 1, 1, 0, missing = 0),
elix_psych = dplyr::if_else(.data$psych_ot >= 2 | .data$psych_ip >= 1, 1, 0, missing = 0),
elix_pulmcirc = dplyr::if_else(.data$pulmcirc_ot >= 2 | .data$pulmcirc_ip >= 1, 1, 0, missing = 0),
elix_renal_mod = dplyr::if_else(.data$renal_mod_ot >= 2 | .data$renal_mod_ip >= 1, 1, 0, missing = 0),
elix_renal_sev = dplyr::if_else(.data$renal_sev_ot >= 2 | .data$renal_sev_ip >= 1, 1, 0, missing = 0),
elix_hypo = dplyr::if_else(.data$hypo_ot >= 2 | .data$hypo_ip >= 1, 1, 0, missing = 0),
elix_thyroid_oth = dplyr::if_else(.data$thyroid_oth_ot >= 2 | .data$thyroid_oth_ip >= 1, 1, 0, missing = 0),
elix_peptic = dplyr::if_else(.data$peptic_ot >= 2 | .data$peptic_ip >= 1, 1, 0, missing = 0),
elix_valve = dplyr::if_else(.data$valve_ot >= 2 | .data$valve_ip >= 1, 1, 0, missing = 0),
elix_weightloss = dplyr::if_else(.data$weightloss_ot >= 2 | .data$weightloss_ip >= 1, 1, 0, missing = 0))
dat2 <- dat_comb %>%
dplyr::select(id, tidyselect::starts_with("elix"))
}
# Final Summary ----
if (version == 9 | version == 19){
dat3 <- dat2 %>%
dplyr::group_by(id) %>%
dplyr::summarize(
elix_chf = max(.data$elix_chf),
elix_valve = max(.data$elix_valve),
elix_pulmcirc = max(.data$elix_pulmcirc),
elix_periph_vasc = max(.data$elix_periph_vasc),
elix_htn_uc = max(.data$elix_htn_uc),
elix_htn_c = max(.data$elix_htn_c),
elix_paralysis = max(.data$elix_paralysis),
elix_neuro = max(.data$elix_neuro),
elix_chronic_pulm = max(.data$elix_chronic_pulm),
elix_diab_uc = max(.data$elix_diab_uc),
elix_diab_c = max(.data$elix_diab_c),
elix_hypo = max(.data$elix_hypo),
elix_renal = max(.data$elix_renal),
elix_liver = max(.data$elix_liver),
elix_peptic = max(.data$elix_peptic),
elix_hiv = max(.data$elix_hiv),
elix_lymph = max(.data$elix_lymph),
elix_mets = max(.data$elix_mets),
elix_tumor = max(.data$elix_tumor),
elix_rheum = max(.data$elix_rheum),
elix_coag = max(.data$elix_coag),
elix_obese = max(.data$elix_obese),
elix_weightloss = max(.data$elix_weightloss),
elix_fluid = max(.data$elix_fluid),
elix_bld_anem = max(.data$elix_bld_anem),
elix_def_anem = max(.data$elix_def_anem),
elix_alcohol = max(.data$elix_alcohol),
elix_drug = max(.data$elix_drug),
elix_psych = max(.data$elix_psych),
elix_depression = max(.data$elix_depression)) %>%
dplyr::ungroup()
dat3 <- dat3 %>%
dplyr::mutate(elix_htn_comb = dplyr::if_else(.data$elix_htn_uc == 1 | .data$elix_htn_c == 1, 1, 0))
dat3 <- dat3 %>%
dplyr::mutate(elix_death = .data$elix_hiv*0 + .data$elix_alcohol*-1 + .data$elix_def_anem*-2 + .data$elix_rheum*0 +
.data$elix_bld_anem*-3 + .data$elix_chf*9 + .data$elix_chronic_pulm*3 + .data$elix_coag*11 +
.data$elix_depression*-5 + .data$elix_diab_uc*0 + .data$elix_diab_c*-3 + .data$elix_drug*-7 +
.data$elix_htn_comb*-1 + .data$elix_hypo*0 + .data$elix_liver*4 + .data$elix_lymph*6 + .data$elix_fluid*11 +
.data$elix_mets*14 + .data$elix_neuro*5 + .data$elix_obese*-5 + .data$elix_paralysis*5 + .data$elix_periph_vasc*3 +
.data$elix_psych*-5 + .data$elix_pulmcirc*6 + .data$elix_renal*6 + .data$elix_tumor*7 + .data$elix_peptic*0 + .data$elix_valve*0 +
.data$elix_weightloss*9,
elix_readmit = .data$elix_hiv*19 + .data$elix_alcohol*6 + .data$elix_def_anem*9 + .data$elix_rheum*4 +
.data$elix_bld_anem*3 + .data$elix_chf*13 + .data$elix_chronic_pulm*8 + .data$elix_coag*7 +
.data$elix_depression*4 + .data$elix_diab_uc*6 + .data$elix_diab_c*9 + .data$elix_drug*14 +
.data$elix_htn_comb*-1 + .data$elix_hypo*0 + .data$elix_liver*10 + .data$elix_lymph*16 + .data$elix_fluid*8 +
.data$elix_mets*21 + .data$elix_neuro*7 + .data$elix_obese*-3 + .data$elix_paralysis*6 + .data$elix_periph_vasc*4 +
.data$elix_psych*10 + .data$elix_pulmcirc*5 + .data$elix_renal*15 + .data$elix_tumor*15 + .data$elix_peptic*0 + .data$elix_valve*0 +
.data$elix_weightloss*10)
}
else{
dat3 <- dat2 %>%
dplyr::group_by(id) %>%
dplyr::summarize(
elix_aids = max(.data$elix_aids),
elix_alcohol = max(.data$elix_alcohol),
elix_def_anem = max(.data$elix_def_anem),
elix_rheum = max(.data$elix_rheum),
elix_bld_loss = max(.data$elix_bld_loss),
elix_cancer_leuk = max(.data$elix_cancer_leuk),
elix_cancer_lymph = max(.data$elix_cancer_lymph),
elix_cancer_mets = max(.data$elix_cancer_mets),
elix_cancer_solid = max(.data$elix_cancer_solid),
elix_cancer_insitu = max(.data$elix_cancer_insitu),
elix_cbvd = max(.data$elix_cbvd),
elix_chf = max(.data$elix_chf),
elix_coag = max(.data$elix_coag),
elix_dementia = max(.data$elix_dementia),
elix_depress = max(.data$elix_depress),
elix_diab_c = max(.data$elix_diab_c),
elix_diab_uc = max(.data$elix_diab_uc),
elix_drug = max(.data$elix_drug),
elix_htn_c = max(.data$elix_htn_c),
elix_htn_uc = max(.data$elix_htn_uc),
elix_liver_mild = max(.data$elix_liver_mild),
elix_liver_sev = max(.data$elix_liver_sev),
elix_chronic_pulm = max(.data$elix_chronic_pulm),
elix_neuro_movt = max(.data$elix_neuro_movt),
elix_neuro_seiz = max(.data$elix_neuro_seiz),
elix_neuro_oth = max(.data$elix_neuro_oth),
elix_obese = max(.data$elix_obese),
elix_paralysis = max(.data$elix_paralysis),
elix_perivasc = max(.data$elix_perivasc),
elix_psych = max(.data$elix_psych),
elix_pulmcirc = max(.data$elix_pulmcirc),
elix_renal_mod = max(.data$elix_renal_mod),
elix_renal_sev = max(.data$elix_renal_sev),
elix_hypo = max(.data$elix_hypo),
elix_thyroid_oth = max(.data$elix_thyroid_oth),
elix_peptic = max(.data$elix_peptic),
elix_valve = max(.data$elix_valve),
elix_weightloss = max(.data$elix_weightloss)) %>%
dplyr::ungroup()
message("Message: Currently there are no weights available for ICD-10.")
}
dat4 <- dat3 %>%
dplyr::select(id, tidyselect::starts_with("elix"))
if (version == 9 | version == 19){
dat4 <- dat4 %>%
dplyr::rename(chf = .data$elix_chf,
valve = .data$elix_valve,
pulmcirc = .data$elix_pulmcirc,
perivasc = .data$elix_periph_vasc,
htn_c = .data$elix_htn_comb,
para = .data$elix_paralysis,
neuro = .data$elix_neuro,
chrnlung = .data$elix_chronic_pulm,
dm = .data$elix_diab_uc,
dmcx = .data$elix_diab_c,
hypothy = .data$elix_hypo,
renlfail = .data$elix_renal,
liver = .data$elix_liver,
ulcer = .data$elix_peptic,
aids = .data$elix_hiv,
lymph = .data$elix_lymph,
mets = .data$elix_mets,
tumor = .data$elix_tumor,
arth = .data$elix_rheum,
coag = .data$elix_coag,
obese = .data$elix_obese,
wghtloss = .data$elix_weightloss,
lytes = .data$elix_fluid,
bldloss = .data$elix_bld_anem,
anemdef = .data$elix_def_anem,
alcohol = .data$elix_alcohol,
drug = .data$elix_drug,
psych = .data$elix_psych,
depress = .data$elix_depression)
}
else{
dat4 <- dat4 %>%
dplyr::rename(aids = .data$elix_aids,
alcohol = .data$elix_alcohol,
anemdef = .data$elix_def_anem,
arth = .data$elix_rheum,
bldloss = .data$elix_bld_loss,
cancer_leuk = .data$elix_cancer_leuk,
cancer_lymph = .data$elix_cancer_lymph,
cancer_mets = .data$elix_cancer_mets,
cancer_nsitu = .data$elix_cancer_insitu,
cancer_solid = .data$elix_cancer_solid,
cbvd = .data$elix_cbvd,
chf = .data$elix_chf,
coag = .data$elix_coag,
dementia = .data$elix_dementia,
depress = .data$elix_depress,
diab_cx = .data$elix_diab_c,
diab_uncx = .data$elix_diab_uc,
drug_abuse = .data$elix_drug,
htn_cx = .data$elix_htn_c,
htn_uncx = .data$elix_htn_uc,
liver_mld = .data$elix_liver_mild,
liver_sev = .data$elix_liver_sev,
lung_chronic = .data$elix_chronic_pulm,
neuro_movt = .data$elix_neuro_movt,
neuro_oth = .data$elix_neuro_seiz,
neuro_seiz = .data$elix_neuro_oth,
obese = .data$elix_obese,
paralysis = .data$elix_paralysis,
perivasc = .data$elix_perivasc,
psychoses = .data$elix_psych,
pulmcirc = .data$elix_pulmcirc,
renlfl_mod = .data$elix_renal_mod,
renlfl_sev = .data$elix_renal_sev,
thyroid_hypo = .data$elix_hypo,
thyroid_oth = .data$elix_thyroid_oth,
ulcer_peptic = .data$elix_peptic,
valve = .data$elix_valve,
wghtloss = .data$elix_weightloss)
}
return(dat4)
}
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Defines functions elixhauser
Documented in elixhauser
#' Elixhauser Comorbidities
#'
#' \code{elixhauser} returns a summary dataset containing the Elixhauser comorbidities for
#' each patient.
#'
#' This function uses data which has been properly prepared to identify and flag the
#' Elixhauser comorbidities. See full package documentation for additional details.
#'
#' @param dat dataset which has been properly prepared using 'prepare_data()'
#' @param id variable of the unique patient identifier
#' @param dx the column with the diagnoses (defaults to 'dx')
#' @param version which version(s) of ICD your data contain (ICD-9 only: 9, ICD-10 only: 10,
#' Both: 19)
#' @param version_var variable which denotes if the diagnoses on that row are ICD-9 (9) or
#' ICD-10 (10)
#' @param outpatient_two whether or not it should be required for there to be two outpatient
#' claims for a diagnosis for a patient to be positively coded with that diagnosis.
#'
#' @return dataframe with one row per patient, and a column for their patient id, a column with each
#' Elixhauser comorbidity, and a column with their Elixhauser index for readmission and death
#'
#' @examples
#' elixhauser(dat = prepared_data, id = patient_id, dx = dx, version = 19,
#' version_var = version, outpatient_two = "yes")
#'
#'
#' @export
#' @importFrom rlang .data
elixhauser <- function(dat = NULL,
id = NULL,
dx = "dx",
version = 19,
version_var = NULL,
outpatient_two = "no"){
id2 <- rlang::quo_name(rlang::enquo(id))
# Elixhauser ICD-9 ----
## Diagnoses Setup ----
if (version == 9){
chf9 <- c("39891", "40201", "40211", "40291", "40401", "40403", "40411", "40413", "40491", "40493",
"4254", "4255", "4257", "4258", "4259")
valve9 <- c("3979", "V422", "V433", "7463", "7464", "7465", "7466")
pulmcirc9 <- c("4179")
periph_vasc9 <- c("44421", "44422", "4471", "449", "4471", "5571", "5579", "V434")
paralysis9 <- c("3449", "78072")
neuro9 <- c("3334", "3335", "33385", "33394", "3452", "3453", "78097", "7843")
chronic_pulm9 <- c("5064")
diab_c9 <- c("7751")
hypo9 <- c("243", "2440", "2441", "2442", "2448", "2449")
renal9 <- c("5853", "5854 ", "5855 ", "5856 ", "5859 ", "586", "V420", "V451", "V4511", "V4512")
liver9 <- c("07022", "07023", "07032", "07033", "07044", "07054", "4560",
"4561", "45620", "45621", "5710", "5712 ", "5713", "5715", "5716",
"5718", "5719", "5723", "5728", "5735", "V427")
peptic9 <- c("53141", "53151", "53161", "53170", "53171", "53191", "53241",
"53251", "53261", "53270", "53271", "53291", "53341", "53351",
"53361", "53370", "53371", "53391", "53441", "53451", "53461",
"53470", "53471", "53491")
mets9 <- c("1990", "1991", "78951")
rheum9 <- c("7010")
coag9 <- c("2871", "28984")
obese9 <- c("2780", "V8554", "79391")
weightloss9 <- c("78321", "78322")
bld_anem9 <- c("2800")
alc9 <- c("2910", "2911", "2912", "2913", "2915", "2919")
drug9 <- c("2920", "2929")
depress9 <- c("3004", "30112", "3090", "3091","311")
chf9_str <- ("428")
valve9_str <- c("424", "0932", "394", "395", "396", "397")
pulmcirc9_str <- c("4151", "416")
periph_vasc9_str <- c("440", "441", "442", "4431", "4432", "4438", "4439")
htn_uc9_str <- c("4011", "4019", "6420")
htn_c9_str <- c("402", "403", "404", "405", "6422", "6421", "6427", "6429")
paralysis9_str <- c("342", "343", "3440", "3441", "3442", "3443", "3444", "3445", "3446", "4382", "4383", "4384", "4385")
neuro9_str <- c("330", "331", "332", "3337", "3334", "3335", "3338", "340", "341","3450", "3451", "3454", "3455", "3456",
"3457", "3458", "3459", "347", "6494", "7687", "7803")
chronic_pulm9_str <- c("490", "491", "492", "493", "494", "495", "496", "500", "501", "502")
diab_uc9_str <- c("2500", "2501", "2502", "2503", "6480", "2490", "2491", "2492", "2493")
diab_c9_str <- c("2504", "2505", "2506", "2507", "2508", "2509", "2494", "2495", "2496", "2497", "2498", "2499")
renal9_str <- c("V560", "V561", "V562", "V563", "V568")
liver9_str <- c("5714")
hiv9_str <- c("042", "043", "044")
lymph9_str <- c("200", "201", "2020", "2021", "2022", "2025", "2026", "2027", "2028", "2029", "203", "2386", "2733")
mets9_str <- c("196", "197", "198", "209")
tumor9_str <- c("14, 15, 16, 170", "171", "172", "174", "175", "179",
"18", "190", "191", "192", "193", "194", "195", "2090", "2091", "2092", "2093", "2580")
rheum9_str <- c("710", "714", "720", "725")
coag9_str <- c("286", "2873", "2874", "2875", "6493")
obese9_str <- c("2780", "6491", "V853", "V854")
weightloss9_str <- c("260", "261", "262", "263")
fluid9_str <- c("276")
bld_anem9_str <- c("6482")
def_anem9_str <- c("280", "2852", "2859")
alcohol9_str <- c("2918", "303", "3050")
drug9_str <- c("2928", "304", "3052", "3053", "3054", "3055", "3056", "3057", "3058", "3059", "6483")
psych9_str <- c("295", "296", "297", "298", "2991")
## Code ----
dat1 <- dat %>%
dplyr::mutate(chf = dplyr::if_else(dx %in% chf9 | stringr::str_starts(dx, paste(chf9_str)), 1, 0),
valve = dplyr::if_else(dx %in% valve9 | stringr::str_starts(dx, paste(valve9_str, sep = "|", collapse = "|")), 1, 0),
pulmcirc = dplyr::if_else(dx %in% pulmcirc9 | stringr::str_starts(dx, paste(pulmcirc9_str, sep = "|", collapse = "|")), 1, 0),
periph_vasc = dplyr::if_else(dx %in% periph_vasc9 | stringr::str_starts(dx, paste(periph_vasc9_str, sep = "|", collapse = "|")), 1, 0),
htn_uc = dplyr::if_else(stringr::str_starts(dx, paste(htn_uc9_str, sep = "|", collapse = "|")), 1, 0),
htn_c = dplyr::if_else(stringr::str_starts(dx, paste(htn_c9_str, sep = "|", collapse = "|")), 1 ,0),
paralysis = dplyr::if_else(dx %in% paralysis9 | stringr::str_starts(dx, paste(paralysis9_str, sep = "|", collapse = "|")), 1, 0),
neuro = dplyr::if_else(dx %in% neuro9 | stringr::str_starts(dx, paste(neuro9_str, sep = "|", collapse = "|")), 1, 0),
chronic_pulm = dplyr::if_else(dx %in% chronic_pulm9 | stringr::str_starts(dx, paste(chronic_pulm9_str, sep = "|", collapse = "|")), 1, 0),
diab_uc = dplyr::if_else(stringr::str_starts(dx, paste(diab_uc9_str, sep = "|", collapse = "|")), 1, 0),
diab_c = dplyr::if_else(dx %in% diab_c9 | stringr::str_starts(dx, paste(diab_c9_str, sep = "|", collapse = "|")), 1, 0),
hypo = dplyr::if_else(dx %in% hypo9, 1, 0),
renal = dplyr::if_else(dx %in% renal9 | stringr::str_starts(dx, paste(renal9_str, sep = "|", collapse = "|")), 1, 0),
liver = dplyr::if_else(dx %in% liver9 | stringr::str_starts(dx, paste(liver9_str)), 1, 0),
peptic = dplyr::if_else(dx %in% peptic9, 1, 0),
hiv = dplyr::if_else(stringr::str_starts(dx, paste(hiv9_str, sep = "|", collapse = "|")), 1 ,0),
lymph = dplyr::if_else(stringr::str_starts(dx, paste(lymph9_str, sep = "|", collapse = "|")), 1, 0),
mets = dplyr::if_else(dx %in% mets9 | stringr::str_starts(dx, paste(mets9_str, sep = "|", collapse = "|")), 1, 0),
tumor = dplyr::if_else(stringr::str_starts(dx, paste(tumor9_str, sep = "|", collapse = "|")), 1, 0),
rheum = dplyr::if_else(dx %in% rheum9 | stringr::str_starts(dx, paste(rheum9_str, sep = "|", collapse = "|")), 1, 0),
coag = dplyr::if_else(dx %in% coag9 | stringr::str_starts(dx, paste(coag9_str, sep = "|", collapse = "|")), 1, 0),
obese = dplyr::if_else(dx %in% obese9 | stringr::str_starts(dx, paste(obese9_str, sep = "|", collapse = "|")), 1, 0),
weightloss = dplyr::if_else(dx %in% weightloss9 | stringr::str_starts(dx, paste(weightloss9_str, sep = "|", collapse = "|")), 1, 0),
fluid = dplyr::if_else(stringr::str_starts(dx, paste(fluid9_str)), 1, 0),
bld_anem = dplyr::if_else(dx %in% bld_anem9 | stringr::str_starts(dx, paste(bld_anem9_str)), 1, 0),
def_anem = dplyr::if_else(stringr::str_starts(dx, paste(def_anem9_str, sep = "|", collapse = "|")), 1, 0),
alcohol = dplyr::if_else(dx %in% alc9 | stringr::str_starts(dx, paste(alcohol9_str, sep = "|", collapse = "|")), 1, 0),
drug = dplyr::if_else(dx %in% drug9 | stringr::str_starts(dx, paste(drug9_str, sep = "|", collapse = "|")), 1, 0),
psych = dplyr::if_else(stringr::str_starts(dx, paste(psych9_str, sep = "|", collapse = "|")), 1, 0),
depression = dplyr::if_else(dx %in% depress9, 1, 0))
dat1 <- dat1 %>%
dplyr::mutate(htn_uc = dplyr::if_else(.data$htn_c == 1, 0, .data$htn_uc),
tumor = dplyr::if_else(.data$mets == 1, 0, .data$tumor),
diab_uc = dplyr::if_else(.data$diab_c == 1, 0, .data$diab_uc),
htn_comb = dplyr::if_else(.data$htn_c == 1 | .data$htn_uc == 1, 1, 0)) }
# Elixhauser ICD-10 ----
else if (version == 10){
## Diagnoses Setup ----
hiv10 <- c("B20", "O98711", "O98712", "O98713", "O98719", "O9872", "O9873",
"Z21")
alcohol10 <- c("F1010", "F1011", "F10120", "F10121", "F10129", "F10130",
"F10131", "F10132", "F10139", "F1014", "F10150", "F10151",
"F10159", "F10180", "F10181", "F10182", "F10188", "F1019",
"F1020", "F1021", "F10220", "F10221", "F10229", "F10230",
"F10231", "F10232", "F10239", "F1024", "F10250", "F10251",
"F10259", "F1026", "F1027", "F10280", "F10281", "F10282",
"F10288", "F1029","F1094","F10950","F10951","F10959", "F1096",
"F1097", "F10980", "G621", "I426", "K2920", "K2921", "O99310",
"O99311", "O99312", "O99313", "O99314", "O99315")
alcohol_liver_mild10 <- c("K7010", "K7011")
def_anem10 <- c("D501", "D508", "D509", "D510", "D511", "D512", "D513", "D518",
"D519", "D520", "D521", "D528", "D529", "D530", "D531", "D532",
"D538", "D539", "D630", "D631", "D638", "D649", "O99011",
"O99012", "O99013", "O99019")
rheum10 <- c("A1801", "A1802", "A3984", "A5441","A5442","L4050","L4051","L4054",
"L4059","L900","L940","L941","L943","M01X0","M01X11", "M01X12",
"M01X19","M01X21", "M01X22", "M01X29", "M01X31", "M01X32", "M01X39",
"M01X41","M01X42","M01X49","M01X51","M01X52","M01X59","M01X61","M01X62",
"M01X69","M01X71","M01X72","M01X79","M01X8","M01X9","M0200","M02011",
"M02012","M02019","M02021","M02022","M02029","M02031","M02032","M02039",
"M02041","M02042","M02049","M02051","M02052","M02059","M02061","M02062",
"M02069","M02071","M02072","M02079","M0208","M0209","M0210","M02111",
"M02112","M02119","M02121","M02122","M02129","M02131","M02132","M02139",
"M02141","M02142","M02149","M02151","M02152","M02159","M02161","M02162",
"M02169","M02171","M02172","M02179","M0218","M0219","M0220","M02211",
"M02212","M02219","M02221","M02222","M02229","M02231","M02232","M02239",
"M02241","M02242","M02249","M02251","M02252","M02259","M02261","M02262",
"M02269","M02271","M02272","M02279","M0228","M0229","M0230","M02311",
"M02312","M02319","M02321","M02322","M02329","M02331","M02332","M02339",
"M02341","M02342","M02349","M02351","M02352","M02359","M02361","M02362",
"M02369","M02371","M02372","M02379","M0238","M0239","M0280","M02811",
"M02812","M02819","M02821","M02822","M02829","M02831","M02832","M02839",
"M02841","M02842","M02849","M02851","M02852","M02859","M02861","M02862",
"M02869","M02871","M02872","M02879","M0288","M0289","M029","M0500","M05011",
"M05012","M05019","M05021","M05022","M05029","M05031","M05032","M05039",
"M05041","M05042","M05049","M05051","M05052","M05059","M05061","M05062",
"M05069","M05071","M05072","M05079","M0509","M0510","M05111","M05112",
"M05119","M05121","M05122","M05129","M05131","M05132","M05139","M05141","
M05142","M05149","M05151","M05152","M05159","M05161","M05162","M05169",
"M05171","M05172","M05179","M0519","M0520","M05211","M05212","M05219",
"M05221","M05222","M05229","M05231","M05232","M05239","M05241","M05242",
"M05249","M05251","M05252","M05259","M05261","M05262","M05269","M05271",
"M05272","M05279","M0529","M0530","M05311","M05312","M05319","M05321",
"M05322","M05329","M05331","M05332","M05339","M05341","M05342","M05349",
"M05351","M05352","M05359","M05361","M05362","M05369","M05371","M05372",
"M05379","M0539","M0540","M05411","M05412","M05419","M05421","M05422",
"M05429","M05431","M05432","M05439","M05441","M05442","M05449","M05451",
"M05452","M05459","M05461","M05462","M05469","M05471","M05472","M05479",
"M0549","M0550","M05511","M05512","M05519","M05521","M05522","M05529",
"M05531","M05532","M05539","M05541","M05542","M05549","M05551","M05552",
"M05559","M05561","M05562","M05569","M05571","M05572","M05579","M0559",
"M0560","M05611","M05612","M05619","M05621","M05622","M05629","M05631",
"M05632","M05639","M05641","M05642","M05649","M05651","M05652","M05659",
"M05661","M05662","M05669","M05671","M05672","M05679","M0569","M0570",
"M05711","M05712","M05719","M05721","M05722","M05729","M05731","M05732",
"M05739","M05741","M05742","M05749","M05751","M05752","M05759","M05761",
"M05762","M05769","M05771","M05772","M05779","M0579","M057A","M0580",
"M05811","M05812","M05819","M05821","M05822","M05829","M05831","M05832",
"M05839","M05841","M05842","M05849","M05851","M05852","M05859","M05861",
"M05862","M05869","M05871","M05872","M05879","M0589","M058A","M059",
"M0600","M06011","M06012","M06019","M06021","M06022","M06029","M06031",
"M06032","M06039","M06041","M06042","M06049","M06051","M06052","M06059",
"M06061","M06062","M06069","M06071","M06072","M06079","M0608","M0609",
"M060A","M061","M0620","M06211","M06212","M06219","M06221","M06222",
"M06229","M06231","M06232","M06239","M06241","M06242","M06249","M06251",
"M06252","M06259","M06261","M06262","M06269","M06271","M06272","M06279",
"M0628","M0629","M0630","M06311","M06312","M06319","M06321","M06322",
"M06329","M06331","M06332","M06339","M06341","M06342","M06349","M06351",
"M06352","M06359","M06361","M06362","M06369","M06371","M06372","M06379",
"M0638","M0639","M064","M0680","M06811","M06812","M06819","M06821",
"M06822","M06829","M06831","M06832","M06839","M06841","M06842","M06849",
"M06851","M06852","M06859","M06861","M06862","M06869","M06871","M06872",
"M06879","M0688","M0689","M068A","M069","M0760","M07611","M07612",
"M07619","M07621","M07622","M07629","M07631","M07632","M07639",
"M07641","M07642","M07649","M07651","M07652","M07659","M07661",
"M07662","M07669","M07671","M07672","M07679","M0768","M0769","M0800",
"M08011","M08012","M08019","M08021","M08022","M08029","M08031","M08032",
"M08039","M08041","M08042","M08049","M08051","M08052","M08059","M08061",
"M08062","M08069","M08071","M08072","M08079","M0808","M0809","M080A","M081",
"M0820","M08211","M08212","M08219","M08221","M08222","M08229","M08231",
"M08232","M08239","M08241","M08242","M08249","M08251","M08252","M08259",
"M08261","M08262","M08269","M08271","M08272","M08279","M0828","M0829",
"M082A","M083","M0840","M08411","M08412","M08419","M08421","M08422",
"M08429","M08431","M08432","M08439","M08441","M08442","M08449","M08451",
"M08452","M08459","M08461","M08462","M08469","M08471","M08472","M08479",
"M0848","M084A","M0880","M08811","M08812","M08819","M08821","M08822",
"M08829","M08831","M08832","M08839","M08841","M08842","M08849","M08851",
"M08852","M08859","M08861","M08862","M08869","M08871","M08872","M08879",
"M0888","M0889","M0890","M08911","M08912","M08919","M08921","M08922",
"M08929","M08931","M08932","M08939","M08941","M08942","M08949","M08951",
"M08952","M08959","M08961","M08962","M08969","M08971","M08972","M08979",
"M0898","M0899","M089A","M1200","M12011","M12012","M12019","M12021","M12022",
"M12029","M12031","M12032","M12039","M12041","M12042","M12049","M12051",
"M12052","M12059","M12061","M12062","M12069","M12071","M12072","M12079",
"M1208","M1209","M300","M301","M302","M303","M308","M310","M311","M312",
"M3130","M3131","M314","M315","M316","M317","M318","M319","M320","M3210",
"M3212","M3213","M3214","M3215","M3219","M328","M329","M3300","M3301","M3302",
"M3303","M3309","M3310","M3311","M3312","M3313","M3319","M3320","M3321","M3322",
"M3329","M3390","M3391","M3392","M3393","M3399","M340","M341","M342",
"M3481","M3482","M3483","M3489","M349","M3500","M3501","M3502",
"M3503","M3504","M3509","M351","M352","M353","M355","M356","M358",
"M359","M360","M361","M368","M450","M451","M452","M453","M454",
"M455","M456","M457","M458","M459","M4600","M4601","M4602","M4603",
"M4604","M4605","M4606","M4607","M4608","M4609","M461","M4650",
"M4651","M4652","M4653","M4654","M4655","M4656","M4657","M4658",
"M4659","M4680","M4681","M4682","M4683","M4684","M4685","M4686",
"M4687","M4688","M4689","M4690","M4691","M4692","M4693","M4694",
"M4695","M4696","M4697","M4698","M4699","M4980","M4981","M4982",
"M4983","M4984","M4985","M4986","M4987","M4988","M4989")
bld_loss10 <- c("D500", "O9081", "O9902", "O9903")
leuk10 <- c("C9010","C9011","C9012","C9100","C9101","C9102","C9110","C9111",
"C9112","C9130","C9131","C9132","C9140","C9141","C9142","C9150",
"C9151","C9152","C9160","C9161","C9162","C9190","C9191","C9192",
"C91A0","C91A1","C91A2","C91Z0","C91Z1","C91Z2","C9200","C9201",
"C9202","C9210","C9211","C9212","C9220","C9221","C9222","C9230",
"C9231","C9232","C9240","C9241","C9242","C9250","C9251","C9252",
"C9260","C9261","C9262","C9290","C9291","C9292","C92A0","C92A1",
"C92A2","C92Z0","C92Z1","C92Z2","C9300","C9301","C9302","C9310",
"C9311","C9312","C9330","C9331","C9332","C9390","C9391","C9392",
"C93Z0","C93Z1","C93Z2","C9400","C9401","C9402","C9420","C9421",
"C9422","C9430","C9431","C9432","C9440","C9441","C9442","C946",
"C9480","C9481","C9482","C9500","C9501","C9502","C9510","C9511",
"C9512","C9590","C9591","C9592")
lymph10 <- c("C8100","C8101","C8102","C8103","C8104","C8105","C8106","C8107",
"C8108","C8109","C8110","C8111","C8112","C8113","C8114","C8115",
"C8116","C8117","C8118","C8119","C8120","C8121","C8122","C8123",
"C8124","C8125","C8126","C8127","C8128","C8129","C8130","C8131",
"C8132","C8133","C8134","C8135","C8136","C8137","C8138","C8139",
"C8140","C8141","C8142","C8143","C8144","C8145","C8146","C8147",
"C8148","C8149","C8170","C8171","C8172","C8173","C8174","C8175",
"C8176","C8177","C8178","C8179","C8190","C8191","C8192","C8193",
"C8194","C8195","C8196","C8197","C8198","C8199","C8200","C8201",
"C8202","C8203","C8204","C8205","C8206","C8207","C8208","C8209",
"C8210","C8211","C8212","C8213","C8214","C8215","C8216","C8217",
"C8218","C8219","C8220","C8221","C8222","C8223","C8224","C8225",
"C8226","C8227","C8228","C8229","C8230","C8231","C8232","C8233",
"C8234","C8235","C8236","C8237","C8238","C8239","C8240","C8241",
"C8242","C8243","C8244","C8245","C8246","C8247","C8248","C8249",
"C8250","C8251","C8252","C8253","C8254","C8255","C8256","C8257",
"C8258","C8259","C8260","C8261","C8262","C8263","C8264","C8265",
"C8266","C8267","C8268","C8269","C8280","C8281","C8282","C8283",
"C8284","C8285","C8286","C8287","C8288","C8289","C8290","C8291",
"C8292","C8293","C8294","C8295","C8296","C8297","C8298","C8299",
"C8300","C8301","C8302","C8303","C8304","C8305","C8306","C8307",
"C8308","C8309","C8310","C8311","C8312","C8313","C8314","C8315",
"C8316","C8317","C8318","C8319","C8330","C8331","C8332","C8333",
"C8334","C8335","C8336","C8337","C8338","C8339","C8350","C8351",
"C8352","C8353","C8354","C8355","C8356","C8357","C8358","C8359",
"C8370","C8371","C8372","C8373","C8374","C8375","C8376","C8377",
"C8378","C8379","C8380","C8381","C8382","C8383","C8384","C8385",
"C8386","C8387","C8388","C8389","C8390","C8391","C8392","C8393",
"C8394","C8395","C8396","C8397","C8398","C8399","C8400","C8401",
"C8402","C8403","C8404","C8405","C8406","C8407","C8408","C8409",
"C8410","C8411","C8412","C8413","C8414","C8415","C8416","C8417",
"C8418","C8419","C8440","C8441","C8442","C8443","C8444","C8445",
"C8446","C8447","C8448","C8449","C8460","C8461","C8462","C8463",
"C8464","C8465","C8466","C8467","C8468","C8469","C8470","C8471",
"C8472","C8473","C8474","C8475","C8476","C8477","C8478","C8479",
"C8490","C8491","C8492","C8493","C8494","C8495","C8496","C8497",
"C8498","C8499","C84A0","C84A1","C84A2","C84A3","C84A4","C84A5",
"C84A6","C84A7","C84A8","C84A9","C84Z0","C84Z1","C84Z2","C84Z3",
"C84Z4","C84Z5","C84Z6","C84Z7","C84Z8","C84Z9","C8510","C8511",
"C8512","C8513","C8514","C8515","C8516","C8517","C8518","C8519",
"C8520","C8521","C8522","C8523","C8524","C8525","C8526","C8527",
"C8528","C8529","C8580","C8581","C8582","C8583","C8584","C8585",
"C8586","C8587","C8588","C8589","C8590","C8591","C8592","C8593",
"C8594","C8595","C8596","C8597","C8598","C8599","C860","C861",
"C862","C863","C864","C865","C866","C880","C882","C883","C884",
"C888","C889","C9000","C9001","C9002","C9020","C9021","C9022",
"C9030","C9031","C9032","C960","C962","C9620","C9621","C9622",
"C9629","C964","C969","C96A","C96Z","D47Z9")
mets10 <- c("C770","C771","C772","C773","C774","C775","C778","C779","C7800",
"C7801","C7802","C781","C782","C7830","C7839","C784","C785","C786",
"C787","C7880","C7889","C7900","C7901","C7902","C7910","C7911",
"C7919","C792","C7931","C7932","C7940","C7949","C7951","C7952",
"C7960","C7961","C7962","C7970","C7971","C7972","C7981","C7982",
"C7989","C799","C7B00","C7B01","C7B02","C7B03","C7B04","C7B09",
"C7B1","C7B8","C800")
insitu10 <- c("D0000","D0001","D0002","D0003","D0004","D0005","D0006","D0007",
"D0008","D001","D002","D010","D011","D012","D013","D0140","D0149",
"D015","D017","D019","D020","D021","D0220","D0221","D0222","D023",
"D024","D030","D0310","D0311","D03111","D03112","D0312","D03121",
"D03122","D0320","D0321","D0322","D0330","D0339","D034","D0351",
"D0352","D0359","D0360","D0361","D0362","D0370","D0371","D0372",
"D038","D039","D040","D0410","D0411","D04111","D04112","D0412",
"D04121","D04122","D0420","D0421","D0422","D0430","D0439","D044",
"D045","D0460","D0461","D0462","D0470","D0471","D0472","D048",
"D049","D0500","D0501","D0502","D0510","D0511","D0512","D0580",
"D0581","D0582","D0590","D0591","D0592","D060","D061","D067",
"D069","D070","D071","D072","D0730","D0739","D074","D075",
"D0760","D0761","D0769","D090","D0910","D0919","D0920","D0921",
"D0922","D093","D098","D099")
solid10 <- c("C000","C001","C002","C003","C004","C005","C006","C008","C009",
"C01","C020","C021","C022","C023","C024","C028","C029","C030",
"C031","C039","C040","C041","C048","C049","C050","C051","C052",
"C058","C059","C060","C061","C062","C0680","C0689","C069","C07",
"C080","C081","C089","C090","C091","C098","C099","C100","C101",
"C102","C103","C104","C108","C109","C110","C111","C112","C113",
"C118","C119","C12","C130","C131","C132","C138","C139","C140",
"C142","C148","C153","C154","C155","C158","C159","C160","C161",
"C162","C163","C164","C165","C166","C168","C169","C170","C171",
"C172","C173","C178","C179","C180","C181","C182","C183","C184",
"C185","C186","C187","C188","C189","C19","C20","C210","C211",
"C212","C218","C220","C221","C222","C223","C224","C227","C228",
"C229","C23","C240","C241","C248","C249","C250","C251","C252",
"C253","C254","C257","C258","C259","C260","C261","C269","C300",
"C301","C310","C311","C312","C313","C318","C319","C320","C321",
"C322","C323","C328","C329","C33","C3400","C3401","C3402","C3410",
"C3411","C3412","C342","C3430","C3431","C3432","C3480","C3481",
"C3482","C3490","C3491","C3492","C37","C380","C381","C382","C383",
"C384","C388","C390","C399","C4000","C4001","C4002","C4010","C4011",
"C4012","C4020","C4021","C4022","C4030","C4031","C4032","C4080",
"C4081","C4082","C4090","C4091","C4092","C410","C411","C412",
"C413","C414","C419","C430","C4310","C4311","C43111","C43112",
"C4312","C43121","C43122","C4320","C4321","C4322","C4330",
"C4331","C4339","C434","C4351","C4352","C4359","C4360","C4361",
"C4362","C4370","C4371","C4372","C438","C439","C4400","C4409",
"C44101","C44102","C441021","C441022","C44109","C441091",
"C441092","C44131","C441321","C441322","C441391","C441392",
"C44191","C44192","C441921","C441922","C44199","C441991",
"C441992","C44201","C44202","C44209","C44291","C44292","C44299",
"C44300","C44301","C44309","C44390","C44391","C44399","C4440",
"C4449","C44500","C44501","C44509","C44590","C44591","C44599",
"C44601","C44602","C44609","C44691","C44692","C44699","C44701",
"C44702","C44709","C44791","C44792","C44799","C4480","C4489",
"C4490","C4499","C450","C451","C452","C457","C459","C460","C461",
"C462","C463","C464","C4650","C4651","C4652","C467","C469","C470",
"C4710","C4711","C4712","C4720","C4721","C4722","C473","C474",
"C475","C476","C478","C479","C480","C481","C482","C488","C490",
"C4910","C4911","C4912","C4920","C4921","C4922","C493","C494",
"C495","C496","C498","C499","C49A0","C49A1","C49A2","C49A3",
"C49A4","C49A5","C49A9","C4A0","C4A10","C4A11","C4A111",
"C4A112","C4A12","C4A121","C4A122","C4A20","C4A21","C4A22",
"C4A30","C4A31","C4A39","C4A4","C4A51","C4A52","C4A59","C4A60",
"C4A61","C4A62","C4A70","C4A71","C4A72","C4A8","C4A9","C50011",
"C50012","C50019","C50021","C50022","C50029","C50111","C50112",
"C50119","C50121","C50122","C50129","C50211","C50212","C50219",
"C50221","C50222","C50229","C50311","C50312","C50319","C50321",
"C50322","C50329","C50411","C50412","C50419","C50421","C50422",
"C50429","C50511","C50512","C50519","C50521","C50522","C50529",
"C50611","C50612","C50619","C50621","C50622","C50629","C50811",
"C50812","C50819","C50821","C50822","C50829","C50911","C50912",
"C50919","C50921","C50922","C50929","C510","C511","C512","C518",
"C519","C52","C530","C531","C538","C539","C540","C541","C542",
"C543","C548","C549","C55","C561","C562","C569","C5700","C5701",
"C5702","C5710","C5711","C5712","C5720","C5721","C5722","C573",
"C574","C577","C578","C579","C58","C600","C601","C602","C608",
"C609","C61","C6200","C6201","C6202","C6210","C6211","C6212","C6290",
"C6291","C6292","C6300","C6301","C6302","C6310","C6311","C6312","C632",
"C637","C638","C639","C641","C642","C649","C651","C652","C659","C661",
"C662","C669","C670","C671","C672","C673","C674","C675","C676","C677",
"C678","C679","C680","C681","C688","C689","C6900","C6901","C6902",
"C6910","C6911","C6912","C6920","C6921","C6922","C6930","C6931",
"C6932","C6940","C6941","C6942","C6950","C6951","C6952","C6960",
"C6961","C6962","C6980","C6981","C6982","C6990","C6991","C6992",
"C700","C701","C709","C710","C711","C712","C713","C714","C715",
"C716","C717","C718","C719","C720","C721","C7220","C7221","C7222",
"C7230","C7231","C7232","C7240","C7241","C7242","C7250","C7259",
"C729","C73","C7400","C7401","C7402","C7410","C7411","C7412",
"C7490","C7491","C7492","C750","C751","C752","C753","C754","C755",
"C758","C759","C760","C761","C762","C763","C7640","C7641","C7642",
"C7650","C7651","C7652","C768","C7A00","C7A010","C7A011","C7A012",
"C7A019","C7A020","C7A021","C7A022","C7A023","C7A024","C7A025",
"C7A026","C7A029","C7A090","C7A091","C7A092","C7A093","C7A094",
"C7A095","C7A096","C7A098","C7A1","C7A8","D469","E3121","E3122",
"E3123")
cbvd_poa10 <- c("G450","G451","G452","G453","G454","G458","G459","G460","G461",
"G462","G463","G464","G465","G466","G467","G468","H3400","H3401",
"H3402","H3403","H3410","H3411","H3412","H3413","H34211","H34212",
"H34213","H34219","H34231","H34232","H34233","H34239","I6000",
"I6001","I6002","I6010","I6011","I6012","I602","I6020","I6021",
"I6022","I6030","I6031","I6032","I604","I6050","I6051","I6052",
"I606","I607","I608","I609","I610","I611","I612","I613","I614",
"I615","I616","I618","I619","I6200","I6203","I621","I629",
"I6300","I63011","I63012","I63013","I63019","I6302","I63031",
"I63032","I63033","I63039","I6309","I6310","I63111","I63112",
"I63113","I63119","I6312","I63131","I63132","I63133","I63139",
"I6319","I6320","I63211","I63212","I63213","I63219","I6322",
"I63231","I63232","I63233","I63239","I6329","I6330","I63311",
"I63312","I63313","I63319","I63321","I63322","I63323","I63329",
"I63331","I63332","I63333","I63339","I63341","I63342","I63343",
"I63349","I6339","I6340","I63411","I63412","I63413","I63419",
"I63421","I63422","I63423","I63429","I63431","I63432","I63433",
"I63439","I63441","I63442","I63443","I63449","I6349","I6350",
"I63511","I63512","I63513","I63519","I63521","I63522","I63523",
"I63529","I63531","I63532","I63533","I63539","I63541","I63542",
"I63543","I63549","I6359","I636","I638","I6381","I6389","I639",
"I6501","I6502","I6503","I6509","I651","I6521","I6522","I6523",
"I6529","I658","I659","I6601","I6602","I6603","I6609","I6611",
"I6612","I6613","I6619","I6621","I6622","I6623","I6629","I663",
"I668","I669")
cbvd_sqla10 <- c("I6930","I6931","I69310","I69311","I69312","I69313","I69314",
"I69315","I69318","I69319","I69320","I69321","I69322","I69323",
"I69328","I69390","I69391","I69392","I69393","I69398","I6980",
"I6981","I69810","I69811","I69812","I69813","I69814","I69815",
"I69818","I69819","I69820","I69821","I69822","I69823","I69828",
"I69890","I69891","I69892","I69893","I69898","I6990","I6991",
"I69910","I69911","I69912","I69913","I69914","I69915","I69918",
"I69919","I69920","I69921","I69922","I69923","I69928","I69990",
"I69991","I69992","I69993","I69998","P91821","P91822","P91823",
"P91829")
cbvd_sqlaparalysis10 <- c("I69331","I69332","I69333","I69334","I69339","I69341",
"I69342","I69343","I69344","I69349","I69351","I69352",
"I69353","I69354","I69359","I69361","I69362","I69363",
"I69364","I69365","I69369","I69831","I69832","I69833",
"I69834","I69839","I69841","I69842","I69843","I69844",
"I69849","I69851","I69852","I69853","I69854","I69859",
"I69861","I69862","I69863","I69864","I69865","I69869",
"I69931","I69932","I69933","I69934","I69939","I69941",
"I69942","I69943","I69944","I69949","I69951","I69952",
"I69953","I69954","I69959","I69961","I69962","I69963",
"I69964","I69965","I69969")
chf10 <- c("I0981","I501","I5020","I5021","I5022","I5023","I5030","I5031","I5032",
"I5033","I5040","I5041","I5042","I5043","I50810","I50811","I50812",
"I50813","I50814","I5082","I5083","I5084","I5089","I509","I5181",
"I97130","I97131","O29121","O29122","O29123","O29129","R570",
"Z95811","Z95812")
chfhtn_cx10 <- c("I110", "I130")
chfhtn_cxrenfl_sev10 <- c("I132")
coag10 <- c("D6109","D611","D612","D613","D61810","D61811","D61818","D6182",
"D6189","D619","D65","D66","D67","D680","D681","D682","D68311",
"D68312","D68318","D6832","D684","D688","D689","D691","D693",
"D6941","D6942","D6949","D6951","D6959","D696","D698","D699",
"D7582","O99111","O99112","O99113","O99119","O9912","O9913")
dementia10 <- c("F0150","F0151","F0280","F0281","F0390","F0391","G300","G301",
"G308","G309","G3101","G3109","G311","G312","G3181","G3182",
"G3183","G3185","G3189","G319")
depress10 <- c("F0631","F0632","F0634","F320","F321","F322","F323","F328",
"F3281","F3289","F329","F330","F331","F332","F333","F338",
"F339","F341")
diab_c10 <- c("E0821","E0822","E0829","E08311","E08319","E08321","E083211",
"E083212","E083213","E083219","E08329","E083291","E083292",
"E083293","E083299","E08331","E083311","E083312","E083313",
"E083319","E08339","E083391","E083392","E083393","E083399",
"E08341","E083411","E083412","E083413","E083419","E08349",
"E083491","E083492","E083493","E083499","E08351","E083511",
"E083512","E083513","E083519","E083521","E083522","E083523",
"E083529","E083531","E083532","E083533","E083539","E083541",
"E083542","E083543","E083549","E083551","E083552","E083553",
"E083559","E08359","E083591","E083592","E083593","E083599",
"E0836","E0837X1","E0837X2","E0837X3","E0837X9","E0839","E0840",
"E0841","E0842","E0843","E0844","E0849","E0851","E0852","E0859",
"E08610","E08618","E08620","E08621","E08622","E08628","E08630",
"E08638","E08641","E08649","E0865","E0869","E088","E0921","E0922",
"E0929","E09311","E09319","E09321","E093211","E093212","E093213","
E093219","E09329","E093291","E093292","E093293","E093299","E09331",
"E093311","E093312","E093313","E093319","E09339","E093391","E093392",
"E093393","E093399","E09341","E093411","E093412","E093413","E093419",
"E09349","E093491","E093492","E093493","E093499","E09351","E093511",
"E093512","E093513","E093519","E093521","E093522","E093523","E093529",
"E093531","E093532","E093533","E093539","E093541","E093542","E093543",
"E093549","E093551","E093552","E093553","E093559","E09359","E093591",
"E093592","E093593","E093599","E0936","E0937X1","E0937X2","E0937X3",
"E0937X9","E0939","E0940","E0941","E0942","E0943","E0944","E0949",
"E0951","E0952","E0959","E09610","E09618","E09620","E09621",
"E09622","E09628","E09630","E09638","E09641","E09649","E0965",
"E0969","E098","E1021","E1022","E1029","E10311","E10319","E10321",
"E103211","E103212","E103213","E103219","E10329","E103291","E103292",
"E103293","E103299","E10331","E103311","E103312","E103313","E103319",
"E10339","E103391","E103392","E103393","E103399","E10341","E103411",
"E103412","E103413","E103419","E10349","E103491","E103492","E103493",
"E103499","E10351","E103511","E103512","E103513","E103519","E103521",
"E103522","E103523","E103529","E103531","E103532","E103533","E103539",
"E103541","E103542","E103543","E103549","E103551","E103552","E103553",
"E103559","E10359","E103591","E103592","E103593","E103599","E1036",
"E1037X1","E1037X2","E1037X3","E1037X9","E1039","E1040","E1041",
"E1042","E1043","E1044","E1049","E1051","E1052","E1059","E10610",
"E10618","E10620","E10621","E10622","E10628","E10630","E10638",
"E10641","E10649","E1065","E1069","E108","E1121","E1122","E1129",
"E11311","E11319","E11321","E113211","E113212","E113213","E113219",
"E11329","E113291","E113292","E113293","E113299","E11331","E113311",
"E113312","E113313","E113319","E11339","E113391","E113392","E113393",
"E113399","E11341","E113411","E113412","E113413","E113419","E11349",
"E113491","E113492","E113493","E113499","E11351","E113511","E113512",
"E113513","E113519","E113521","E113522","E113523","E113529","E113531",
"E113532","E113533","E113539","E113541","E113542","E113543","E113549",
"E113551","E113552","E113553","E113559","E11359","E113591","E113592",
"E113593","E113599","E1136","E1137X1","E1137X2","E1137X3","E1137X9",
"E1139","E1140","E1141","E1142","E1143","E1144","E1149","E1151",
"E1152","E1159","E11610","E11618","E11620","E11621","E11622","
E11628","E11630","E11638","E11641","E11649","E1165","E1169","E118",
"E1321","E1322","E1329","E13311","E13319","E13321","E133211","E133212",
"E133213","E133219","E13329","E133291","E133292","E133293","E133299",
"E13331","E133311","E133312","E133313","E133319","E13339","E133391",
"E133392","E133393","E133399","E13341","E133411","E133412","E133413",
"E133419","E13349","E133491","E133492","E133493","E133499","E13351",
"E133511","E133512","E133513","E133519","E133521","E133522","E133523",
"E133529","E133531","E133532","E133533","E133539","E133541","E133542",
"E133543","E133549","E133551","E133552","E133553","E133559","E13359",
"E133591","E133592","E133593","E133599","E1336","E1337X1","E1337X2",
"E1337X3","E1337X9","E1339","E1340","E1341","E1342","E1343","E1344",
"E1349","E1351","E1352","E1359","E13610","E13618","E13620","E13621",
"E13622","E13628","E13630","E13638","E13641","E13649","E1365","E1369",
"E138")
diab_uc10 <- c("E0800","E0801","E0810","E0811","E089","E0900","E0901","E0910",
"E0911","E099","E1010","E1011","E109","E1100","E1101","E1110",
"E1111","E119","E1300","E1301","E1310","E1311","E139","O24011",
"O24012","O24013","O24019","O2402","O2403","O24111","O24112",
"O24113","O24119","O2412","O2413","O24311","O24312","O24313",
"O24319","O2432","O2433","O24410","O24414","O24415","O24419",
"O24420","O24424","O24425","O24429","O24430","O24434","O24435",
"O24439","O24811","O24812","O24813","O24819","O2482","O2483",
"O24911","O24912","O24913","O24919","O2492","O2493")
drug10 <- c("F1110","F1111","F11120","F11121","F11122","F11129","F1113","F1114",
"F11181","F11182","F11188","F1119","F1120","F1121","F11220","F11221",
"F11222","F11229","F1123","F1124","F11281","F11282","F11288","F1129",
"F1210","F1211","F12120","F12121","F12122","F12129","F1213","F12180",
"F12188","F1219","F1220","F1221","F12220","F12221","F12222","F12229",
"F1223","F12280","F12288","F1229","F1310","F1311","F13120","F13121",
"F13129","F13130","F13131","F13132","F13139","F1314","F13180","F13181",
"F13182","F13188","F1319","F1320","F1321","F13220","F13221","F13229",
"F13230","F13231","F13232","F13239","F1324","F1326","F1327","F13280",
"F13281","F13282","F13288","F1329","F1410","F1411","F14120","F14121",
"F14122","F14129","F1413","F1414","F14180","F14181","F14182","F14188",
"F1419","F1420","F1421","F14220","F14221","F14222","F14229","F1423",
"F1424","F14280","F14281","F14282","F14288","F1429","F1510","F1511",
"F15120","F15121","F15122","F15129","F1513","F1514","F15180","F15181",
"F15182","F15188","F1519","F1520","F1521","F15220","F15221","F15222",
"F15229","F1523","F1524","F15280","F15281","F15282","F15288","F1529",
"F1610","F1611","F16120","F16121","F16122","F16129","F1614","F16180",
"F16183","F16188","F1619","F1620","F1621","F16220","F16221","F16229",
"F1624","F16280","F16283","F16288","F1629","F1810","F1811","F18120",
"F18121","F18129","F1814","F1817","F18180","F18188","F1819","F1820",
"F1821","F18220","F18221","F18229","F1824","F1827","F18280","F18288",
"F1829","F1910","F1911","F19120","F19121","F19122","F19129","F19130",
"F19131","F19132","F19139","F1914","F1916","F1917","F19180","F19181",
"F19182","F19188","F1919","F1920","F1921","F19220","F19221","F19222",
"F19229","F19230","F19231","F19232","F19239","F1924","F1926","F1927",
"F19280","F19281","F19282","F19288","F1929","O99320","O99321",
"O99322","O99323","O99324","O99325")
drug_psych10 <- c("F11150","F11151","F11159","F11250","F11251","F11259",
"F12150","F12151","F12159","F12250","F12251","F12259",
"F13150","F13151","F13159","F13250","F13251","F13259",
"F14150","F14151","F14159","F14250","F14251","F14259",
"F15150","F15151","F15159","F15250","F15251","F15259",
"F16150","F16151","F16159","F16250","F16251","F16259",
"F18150","F18151","F18159","F18250","F18251","F18259",
"F19150","F19151","F19159","F19250","F19251","F19259")
htn_c10 <- c("H35031","H35032","H35033","H35039","I119","I129","I1310","I150",
"I151","I152","I158","I159","I161","I674","O10111","O10112",
"O10113","O10119","O1012","O1013","O10211","O10212","O10213",
"O10219","O1022","O1023","O10311","O10312","O10313","O10319",
"O1032","O1033","O10411","O10412","O10413","O10419","O1042",
"O1043","O10911","O10912","O10913","O10919","O1092","O1093",
"O111","O112","O113","O114","O115","O119","O161","O162","O163",
"O164","O165","O169")
htn_cxrenlfl_sv10 <- c("I120", "I1311")
htn_uc10 <- c("I10","I160","I169","O10011","O10012","O10013","O10019","O1002",
"O1003")
liver_mild10 <- c("A5145","A5274","B180","B181","B182","B188","B189","B1910",
"B1920","B199","B251","B581","K700","K702","K7030","K7031",
"K709","K713","K714","K7150","K7151","K716","K717","K718",
"K730","K731","K732","K738","K739","K740","K7400","K7401",
"K7402","K741","K742","K743","K744","K745","K7460","K7469",
"K751","K752","K753","K754","K7581","K7589","K759","K760",
"K761","K762","K763","K764","K7681","K7689","K769","K77")
liver_sev10 <- c("B190","B1911","B1921","I8500","I8501","I8510","I8511","I864",
"K7040","K7041","K7210","K7211","K7290","K7291","K765","K766",
"K767","K9182","Z944")
chronic_pulm10 <- c("J410","J411","J418","J42","J430","J431","J432","J438",
"J439","J440","J441","J449","J4520","J4521","J4522",
"J4530","J4531","J4532","J4540","J4541","J4542","J4550",
"J4551","J4552","J45901","J45902","J45909","J45990",
"J45991","J45998","J470","J471","J479","J60","J61",
"J620","J628","J630","J631","J632","J633","J634",
"J635","J636","J64","J65","J660","J661","J662","J668","J670",
"J671","J672","J673","J674","J675","J676","J677","J678",
"J679","J684","J701","J703")
neuro_mvt10 <- c("G08","G10","G110","G111","G1110","G1111","G1119","G112",
"G113","G114","G118","G119","G120","G121","G1220","G1221",
"G1222","G1223","G1224","G1225","G1229","G128","G129","G130",
"G131","G132","G138","G20","G210","G2111","G2119","G212",
"G213","G214","G218","G219","G230","G231","G232","G238",
"G239","G2409","G241","G242","G248","G254","G255","G2570",
"G2571","G2579","G2581","G2582","G2583","G2589","G259","G26",
"G320","G3281","G3289","G803")
neuro_oth10 <- c("E7500","E7501","E7502","E7509","E7510","E7511","E7519","E7523",
"E7525","E7526","E7529","E754","F05","F842","G35","G360","G368",
"G369","G370","G371","G372","G373","G374","G375","G378","G379",
"G47411","G47419","G47421","G47429","G890","G910","G911","G912",
"G913","G914","G918","G919","G930","G9340","G9341","G9349",
"G935","G936","G937","G9381","G9382","G9389","G939","G94",
"O99350","O99351","O99352","O99353","O99354","O99355","P9160",
"P9161","P9162","P9163")
neuro_seiz10 <- c("G40001","G40009","G40011","G40019","G40101","G40109","G40111",
"G40119","G40201","G40209","G40211","G40219","G40301","G40309",
"G40311","G40319","G40401","G40409","G40411","G40419","G4042",
"G40501","G40509","G40801","G40802","G40803","G40804","G40811",
"G40812","G40813","G40814","G40821","G40822","G40823","G40824",
"G40833","G40834","G4089","G40901","G40909","G40911","G40919",
"G40A01","G40A09","G40A11","G40A19","G40B01","G40B09","G40B11",
"G40B19","R561","R569")
obese10 <- c("E6601","E6609","E661","E662","E668","E669","O99210","O99211",
"O99212","O99213","O99214","O99215","R939","Z6830","Z6831","Z6832",
"Z6833","Z6834","Z6835","Z6836","Z6837","Z6838","Z6839","Z6841",
"Z6842","Z6843","Z6844","Z6845","Z6854")
paralysis10 <- c("G041","G800","G801","G802","G808","G809","G8100","G8101",
"G8102","G8103","G8104","G8110","G8111","G8112","G8113",
"G8114","G8190","G8191","G8192","G8193","G8194","G8220","G8221",
"G8222","G8250","G8251","G8252","G8253","G8254","G830","G8310",
"G8311","G8312","G8313","G8314","G8320","G8321","G8322","G8323",
"G8324","G8330","G8331","G8332","G8333","G8334","G834","G835",
"G8381","G8382","G8383","G8384","G8389","G839","I69031",
"I69032","I69033","I69034","I69039","I69041","I69042","I69043",
"I69044","I69049","I69051","I69052","I69053","I69054","I69059",
"I69061","I69062","I69063","I69064","I69065","I69069","I69131",
"I69132","I69133","I69134","I69139","I69141","I69142","I69143",
"I69144","I69149","I69151","I69152","I69153","I69154","I69159",
"I69161","I69162","I69163","I69164","I69165","I69169","I69231",
"I69232","I69233","I69234","I69239","I69241","I69242","I69243",
"I69244","I69249","I69251","I69252","I69253","I69254","I69259",
"I69261","I69262","I69263","I69264","I69265","I69269","R532")
periph_vasc10 <- c("A5200","A5201","A5202","A5209","I700","I701","I70201",
"I70202","I70203","I70208","I70209","I70211","I70212",
"I70213","I70218","I70219","I70221","I70222","I70223",
"I70228","I70229","I70231","I70232","I70233","I70234",
"I70235","I70238","I70239","I70241","I70242","I70243",
"I70244","I70245","I70248","I70249","I7025","I70261",
"I70262","I70263","I70268","I70269","I70291","I70292",
"I70293","I70298","I70299","I70301","I70302","I70303",
"I70308","I70309","I70311","I70312","I70313","I70318",
"I70319","I70321","I70322","I70323","I70328","I70329",
"I70331","I70332","I70333","I70334","I70335","I70338",
"I70339","I70341","I70342","I70343","I70344","I70345",
"I70348","I70349","I7035","I70361","I70362","I70363",
"I70368","I70369","I70391","I70392","I70393","I70398",
"I70399","I70401","I70402","I70403","I70408","I70409",
"I70411","I70412","I70413","I70418","I70419","I70421",
"I70422","I70423","I70428","I70429","I70431","I70432",
"I70433","I70434","I70435","I70438","I70439","I70441",
"I70442","I70443","I70444","I70445","I70448","I70449",
"I7045","I70461","I70462","I70463","I70468","I70469",
"I70491","I70492","I70493","I70498","I70499","I70501",
"I70502","I70503","I70508","I70509","I70511","I70512",
"I70513","I70518","I70519","I70521","I70522","I70523",
"I70528","I70529","I70531","I70532","I70533","I70534",
"I70535","I70538","I70539","I70541","I70542","I70543",
"I70544","I70545","I70548","I70549","I7055","I70561",
"I70562","I70563","I70568","I70569","I70591","I70592",
"I70593","I70598","I70599","I70601","I70602","I70603",
"I70608","I70609","I70611","I70612","I70613","I70618",
"I70619","I70621","I70622","I70623","I70628","I70629",
"I70631","I70632","I70633","I70634","I70635","I70638",
"I70639","I70641","I70642","I70643","I70644","I70645",
"I70648","I70649","I7065","I70661","I70662","I70663",
"I70668","I70669","I70691","I70692","I70693","I70698",
"I70699","I70701","I70702","I70703","I70708","I70709",
"I70711","I70712","I70713","I70718","I70719","I70721",
"I70722","I70723","I70728","I70729","I70731","I70732",
"I70733","I70734","I70735","I70738","I70739","I70741",
"I70742","I70743","I70744","I70745","I70748","I70749",
"I7075","I70761","I70762","I70763","I70768","I70769",
"I70791","I70792","I70793","I70798","I70799","I708",
"I7090","I7091","I7092","I7100","I7101","I7102","I7103",
"I711","I712","I713","I714","I715","I716","I718","I719",
"I720","I721","I722","I723","I724","I725","I726","I728",
"I729","I7301","I731","I7381","I7389","I739","I7401",
"I7409","I7410","I7411","I7419","I742","I743","I744",
"I745","I748","I749","I75011","I75012","I75013","I75019",
"I75021","I75022","I75023","I75029","I7581","I7589","I770",
"I771","I772","I773","I774","I775","I776","I7770","I7771",
"I7772","I7773","I7774","I7775","I7776","I7777","I7779",
"I77810","I77811","I77812","I77819","I7789","I779","I780",
"I781","I788","I789","I790","I791","I798","I998","I999",
"K31811","K31819","K551","K558","K559","Z95820","Z95828")
psych10 <- c("F060","F061","F062","F0630","F0633","F11950","F11951","F11959",
"F12950","F12951","F12959","F13950","F13951","F13959","F14950",
"F14951","F14959","F15950","F15951","F15959","F16950","F16951",
"F16959","F18950","F18951","F18959","F19950","F19951","F19959",
"F200","F201","F202","F203","F205","F2081","F2089","F209","F21",
"F22","F23","F24","F250","F251","F258","F259","F28","F29","F3010",
"F3011","F3012","F3013","F302","F303","F304","F308","F309","F310",
"F3110","F3111","F3112","F3113","F312","F3130","F3131","F3132",
"F314","F315","F3160","F3161","F3162","F3163","F3164","F3170",
"F3171","F3172","F3173","F3174","F3175","F3176","F3177","F3178",
"F3181","F3189","F319","F324","F325","F3340","F3341","F3342",
"F340","F348","F3481","F3489","F349","F39","F4489","F843")
pulmcirc10 <- c("I270","I271","I272","I2720","I2721","I2722","I2723","I2724",
"I2729","I2781","I2782","I2783","I2789","I279","I280","I281",
"I288","I289")
renal_mod10 <- c("N183","N1830","N1831","N1832","N189","N19")
renal_sev10 <- c("N184","N185","N186","Z4901","Z4902","Z4931","Z4932","Z9115",
"Z940","Z992")
hypo10 <- c("E000","E001","E002","E009","E010","E011","E012","E018","E02",
"E030","E031","E032","E033","E034","E035","E038","E039","E890")
thy_oth10 <- c("E040","E041","E042","E048","E049","E0500","E0501","E0510",
"E0511","E0520","E0521","E0530","E0531","E0540","E0541","E0580",
"E0581","E0590","E0591","E060","E061","E062","E063","E064",
"E065","E069","O905")
peptic10 <- c("K250","K251","K252","K253","K254","K255","K256","K257","K259",
"K260","K261","K262","K263","K264","K265","K266","K267","K269",
"K270","K271","K272","K273","K274","K275","K276","K277","K279",
"K280","K281","K282","K283","K284","K285","K286","K287","K289")
valve10 <- c("A1884","A3282","A3951","A5203","B3321","B376","I011","I018",
"I019","I020","I050","I051","I052","I058","I059","I060","I061",
"I062","I068","I069","I070","I071","I072","I078","I079","I080",
"I081","I082","I083","I088","I089","I091","I0989","I330","I339",
"I340","I341","I342","I348","I349","I350","I351","I352","I358",
"I359","I360","I361","I362","I368","I369","I370","I371","I372",
"I378","I379","I38","I39","M3211","Q220","Q221","Q222","Q223",
"Q224","Q225","Q226","Q228","Q229","Q230","Q231","Q232","Q233",
"Q234","Q238","Q239","T8201XA","T8201XD","T8201XS","T8202XA",
"T8202XD","T8202XS","T8203XA","T8203XD","T8203XS","T8209XA",
"T8209XD","T8209XS","T82221A","T82221D","T82221S","T82222A",
"T82222D","T82222S","T82223A","T82223D","T82223S","T82228A",
"T82228D","T82228S","T826XXA","T826XXD","T826XXS","Z952",
"Z953","Z954")
weightloss10 <- c("E40","E41","E42","E43","E440","E441","E45","E46","E640","O2510",
"O2511","O2512","O2513","O252","O253","R634","R64")
# Code ----
dat1 <- dat %>%
dplyr::mutate(aids = dplyr::if_else(dx %in% hiv10, 1, 0),
alcohol = dplyr::if_else(dx %in% alcohol10 | dx %in% alcohol_liver_mild10, 1, 0),
def_anem = dplyr::if_else(dx %in% def_anem10, 1, 0),
rheum = dplyr::if_else(dx %in% rheum10, 1, 0),
bld_loss = dplyr::if_else(dx %in% bld_loss10, 1, 0),
cancer_leuk = dplyr::if_else(dx %in% leuk10, 1, 0),
cancer_lymph = dplyr::if_else(dx %in% lymph10, 1, 0),
cancer_mets = dplyr::if_else(dx %in% mets10, 1, 0),
cancer_solid = dplyr::if_else(dx %in% solid10, 1, 0),
cancer_insitu = dplyr::if_else(dx %in% insitu10, 1, 0),
cbvd = dplyr::if_else(dx %in% cbvd_poa10 | dx %in% cbvd_sqla10, 1, 0),
chf = dplyr::if_else(dx %in% chf10, 1, 0),
coag = dplyr::if_else(dx %in% coag10, 1, 0),
dementia = dplyr::if_else(dx %in% dementia10, 1, 0),
depress = dplyr::if_else(dx %in% depress10, 1, 0),
diab_c = dplyr::if_else(dx %in% diab_c10, 1, 0),
diab_uc = dplyr::if_else(dx %in% diab_uc10, 1, 0),
drug = dplyr::if_else(dx %in% drug10 | dx %in% drug_psych10, 1, 0),
htn_c = dplyr::if_else(dx %in% htn_c10 | dx %in% chfhtn_cx10 | dx %in% chfhtn_cxrenfl_sev10, 1, 0),
htn_uc = dplyr::if_else(dx %in% htn_uc10, 1, 0),
liver_mild = dplyr::if_else(dx %in% liver_mild10, 1, 0),
liver_sev = dplyr::if_else(dx %in% liver_sev10, 1, 0),
chronic_pulm = dplyr::if_else(dx %in% chronic_pulm10, 1, 0),
neuro_movt = dplyr::if_else(dx %in% neuro_mvt10, 1, 0),
neuro_seiz = dplyr::if_else(dx %in% neuro_seiz10, 1, 0),
neuro_oth = dplyr::if_else(dx %in% neuro_oth10, 1, 0),
obese = dplyr::if_else(dx %in% obese10, 1, 0),
paralysis = dplyr::if_else(dx %in% paralysis10 | dx %in% cbvd_sqlaparalysis10, 1, 0),
perivasc = dplyr::if_else(dx %in% periph_vasc10, 1, 0),
psych = dplyr::if_else(dx %in% psych10, 1, 0),
pulmcirc = dplyr::if_else(dx %in% pulmcirc10, 1, 0),
renal_mod = dplyr::if_else(dx %in% renal_mod10, 1, 0),
renal_sev = dplyr::if_else(dx %in% renal_sev10, 1, 0),
hypo = dplyr::if_else(dx %in% hypo10, 1, 0),
thyroid_oth = dplyr::if_else(dx %in% thy_oth10, 1, 0),
peptic = dplyr::if_else(dx %in% peptic10, 1, 0),
valve = dplyr::if_else(dx %in% valve10, 1, 0),
weightloss = dplyr::if_else(dx %in% weightloss10, 1, 0))
dat1 <- dat1 %>%
dplyr::mutate(diab_uc = dplyr::if_else(.data$diab_c == 1, 0, .data$diab_uc),
htn_uc = dplyr::if_else(.data$htn_c == 1, 0, .data$htn_c),
cancer_solid = dplyr::if_else(.data$cancer_mets == 1, 0, .data$cancer_solid),
cancer_insitu = dplyr::if_else(.data$cancer_mets == 1, 0, .data$cancer_insitu),
cancer_insitu = dplyr::if_else(.data$cancer_solid == 1, 0, .data$cancer_insitu),
liver_mild = dplyr::if_else(.data$liver_sev == 1, 0, .data$liver_mild),
renal_mild = dplyr::if_else(.data$renal_sev == 1, 0, .data$renal_sev))
}
# Elixhauser Both ----
else if (version == 19){
message("Message: Specifying that your data uses both ICD-9 and ICD-10 will result in only the Elixhauser comorbidities \n which are compatible with ICD-9, as the changes and additions which are seen in \n ICD-10 have, to date, not been back-mapped to ICD-9.")
## Diagnoses Setup ----
chf9 <- c("39891", "40201", "40211", "40291", "40401", "40403", "40411", "40413", "40491", "40493",
"4254", "4255", "4257", "4258", "4259")
valve9 <- c("3979", "V422", "V433", "7463", "7464", "7465", "7466")
pulmcirc9 <- c("4179")
periph_vasc9 <- c("44421", "44422", "4471", "449", "4471", "5571", "5579", "V434")
paralysis9 <- c("3449", "78072")
neuro9 <- c("3334", "3335", "33385", "33394", "3452", "3453", "78097", "7843")
chronic_pulm9 <- c("5064")
diab_c9 <- c("7751")
hypo9 <- c("243", "2440", "2441", "2442", "2448", "2449")
renal9 <- c("5853", "5854 ", "5855 ", "5856 ", "5859 ", "586", "V420", "V451", "V4511", "V4512")
liver9 <- c("07022", "07023", "07032", "07033", "07044", "07054", "4560",
"4561", "45620", "45621", "5710", "5712 ", "5713", "5715", "5716",
"5718", "5719", "5723", "5728", "5735", "V427")
peptic9 <- c("53141", "53151", "53161", "53170", "53171", "53191", "53241",
"53251", "53261", "53270", "53271", "53291", "53341", "53351",
"53361", "53370", "53371", "53391", "53441", "53451", "53461",
"53470", "53471", "53491")
mets9 <- c("1990", "1991", "78951")
rheum9 <- c("7010")
coag9 <- c("2871", "28984")
obese9 <- c("2780", "V8554", "79391")
weightloss9 <- c("78321", "78322")
bld_anem9 <- c("2800")
alc9 <- c("2910", "2911", "2912", "2913", "2915", "2919")
drug9 <- c("2920", "2929")
depress9 <- c("3004", "30112", "3090", "3091", "311")
chf9_str <- ("428")
valve9_str <- c("424", "0932", "394", "395", "396", "397")
pulmcirc9_str <- c("4151", "416")
periph_vasc9_str <- c("440", "441", "442", "4431", "4432", "4438", "4439")
htn_uc9_str <- c("4011", "4019", "6420")
htn_c9_str <- c("402", "403", "404", "405", "6422", "6421", "6427", "6429")
paralysis9_str <- c("342", "343", "3440", "3441", "3442", "3443", "3444", "3445", "3446", "4382", "4383", "4384", "4385")
neuro9_str <- c("330", "331", "332", "3337", "3334", "3335", "3338", "340", "341","3450", "3451", "3454", "3455", "3456",
"3457", "3458", "3459", "347", "6494", "7687", "7803")
chronic_pulm9_str <- c("490", "491", "492", "493", "494", "495", "496", "500", "501", "502")
diab_uc9_str <- c("2500", "2501", "2502", "2503", "6480", "2490", "2491", "2492", "2493")
diab_c9_str <- c("2504", "2505", "2506", "2507", "2508", "2509", "2494", "2495", "2496", "2497", "2498", "2499")
renal9_str <- c("V560", "V561", "V562", "V563", "V568")
liver9_str <- c("5714")
hiv9_str <- c("042", "043", "044")
lymph9_str <- c("200", "201", "2020", "2021", "2022", "2025", "2026", "2027", "2028", "2029", "203", "2386", "2733")
mets9_str <- c("196", "197", "198", "209")
tumor9_str <- c("14, 15, 16, 170", "171", "172", "174", "175", "179",
"18", "190", "191", "192", "193", "194", "195", "2090", "2091", "2092", "2093", "2580")
rheum9_str <- c("710", "714", "720", "725")
coag9_str <- c("286", "2873", "2874", "2875", "6493")
obese9_str <- c("2780", "6491", "V853", "V854")
weightloss9_str <- c("260", "261", "262", "263")
fluid9_str <- c("276")
bld_anem9_str <- c("6482")
def_anem9_str <- c("280", "2852", "2859")
alcohol9_str <- c("2918", "303", "3050")
drug9_str <- c("2928", "304", "3052", "3053", "3054", "3055", "3056", "3057", "3058", "3059", "6483")
psych9_str <- c("295", "296", "297", "298", "2991")
chf10beta <- c("I0981","I501","I5020","I5021","I5022","I5023","I5030",
"I5031","I5032","I5033","I5040","I5041","I5042","I5043",
"I50810","I50811","I50812","I50813","I50814","I5082",
"I5083","I5084","I5089","I509","I130") # hhrwchf
valve10beta <- c("A5203","I050","I051","I052","I058","I059","I060","I061",
"I062","I068","I069","I070","I071","I072","I078","I079",
"I080","I081","I082","I083","I088","I089","I091","I0989",
"I340","I341","I342","I348","I349","I350","I351","I352",
"I358","I359","I360","I361","I362","I368","I369","I370",
"I371","I372","I378","I379","I38","I39","Q230","Q231",
"Q232","Q233","Z952","Z953","Z954")
pulmcirc10beta <- c("I2601","I2602","I2609","I2690","I2692","I2693",
"I2694","I2699","I270","I271","I2781","I2782","I2783",
"I2789","I279","I289","T800XXA","T82817A","T82818A")
periph_vasc10beta <- c("I700","I701","I70201","I70202","I70203","I70208",
"I70209","I70211","I70212","I70213","I70218","I70219",
"I70221","I70222","I70223","I70228","I70229","I70231",
"I70232","I70233","I70234","I70235","I70238","I70239",
"I70241","I70242","I70243","I70244","I70245","I70248",
"I70249","I7025","I70261","I70262","I70263","I70268",
"I70269","I70291","I70292","I70293","I70298","I70299",
"I70301","I70302","I70303","I70308","I70309","I70311",
"I70312","I70313","I70318","I70319","I70321","I70322",
"I70323","I70328","I70329","I70331","I70332","I70333",
"I70334","I70335","I70338","I70339","I70341","I70342",
"I70343","I70344","I70345","I70348","I70349","I7035",
"I70361","I70362","I70363","I70368","I70369","I70391",
"I70392","I70393","I70398","I70399","I70401","I70402",
"I70403","I70408","I70409","I70411","I70412","I70413",
"I70418","I70419","I70421","I70422","I70423","I70428",
"I70429","I70431","I70432","I70433","I70434","I70435",
"I70438","I70439","I70441","I70442","I70443","I70444",
"I70445","I70448","I70449","I7045","I70461","I70462",
"I70463","I70468","I70469","I70491","I70492","I70493",
"I70498","I70499","I70501","I70502","I70503","I70508",
"I70509","I70511","I70512","I70513","I70518","I70519",
"I70521","I70522","I70523","I70528","I70529","I70531",
"I70532","I70533","I70534","I70535","I70538","I70539",
"I70541","I70542","I70543","I70544","I70545","I70548",
"I70549","I7055","I70561","I70562","I70563","I70568",
"I70569","I70591","I70592","I70593","I70598","I70599",
"I70601","I70602","I70603","I70608","I70609","I70611",
"I70612","I70613","I70618","I70619","I70621","I70622",
"I70623","I70628","I70629","I70631","I70632","I70633",
"I70634","I70635","I70638","I70639","I70641","I70642",
"I70643","I70644","I70645","I70648","I70649","I7065",
"I70661","I70662","I70663","I70668","I70669","I70691",
"I70692","I70693","I70698","I70699","I70701","I70702",
"I70703","I70708","I70709","I70711","I70712","I70713",
"I70718","I70719","I70721","I70722","I70723","I70728"
,"I70729","I70731","I70732","I70733","I70734","I70735",
"I70738","I70739","I70741","I70742","I70743","I70744",
"I70745","I70748","I70749","I7075","I70761","I70762",
"I70763","I70768","I70769","I70791","I70792","I70793",
"I70798","I70799","I708","I7090","I7091","I7092","I7100",
"I7101","I7102","I7103","I711","I712","I713","I714",
"I715","I716","I718","I719","I720","I721","I722","I723",
"I724","I725","I726","I728","I729","I731","I7381",
"I7389","I739","I742","I743","I744","I76","I771",
"I7770","I7771","I7772","I7773","I7774","I7775",
"I7776","I7777","I7779","I790","I791","I798","K551",
"K558","K559","Z95820","Z95828")
htn_uc10beta <- c("I10", "O10011","O10012","O10013","O10019","O1002","O1003",
"O10911","O10912","O10913","O10919","O1092","O1093")
htn_c10beta <- c("I160","I161","I169","I674",
"I130", # hhrwchf
"I1310", # hhrwohrf
"I129", #hrenworf
"I150", #hrenworf
"I151", #hrenworf
"I120", #hrnwrf
"O10111", #htnpreg
"O10112","O10113","O10119","O1012","O1013","O10211",
"O10212","O10213","O10219","O1022","O1023","O10311",
"O10312","O10313","O10319","O1032","O1033","O10411",
"O10412","O10413","O10419","O1042","O1043","O111","O112",
"O113","O114","O115","O119",
"O161", # ohtnpreg
"O162",
"O163",
"O164",
"O165",
"O169",
"I110", #htnwchf
"I110", #htnwchf
"I119", #htnwochf
"I152", "I158", "I159")
paralysis10beta <- c("G041","G800","G801","G802","G804","G808","G809",
"G8100","G8101","G8102","G8103","G8104","G8110",
"G8111","G8112","G8113","G8114","G8190","G8191",
"G8192","G8193","G8194","G8220","G8221","G8222",
"G8250","G8251","G8252","G8253","G8254","G830","
G8310","G8311","G8312","G8313","G8314","G8320","G8321",
"G8322","G8323","G8324","G8330","G8331","G8332","G8333",
"G8334","G834","G835","G8381","G8382","G8383","G8384",
"G8389","G839","I69031","I69032","I69033","I69034",
"I69039","I69041","I69042","I69043","I69044","I69049",
"I69051","I69052","I69053","I69054","I69059","I69061",
"I69062","I69063","I69064","I69065","I69069","I69131","
I69132","I69133","I69134","I69139","I69141","I69142",
"I69143","I69144","I69149","I69151","I69152","I69153",
"I69154","I69159","I69161","I69162","I69163","I69164",
"I69165","I69169","I69231","I69232","I69233","I69234",
"I69239","I69241","I69242","I69243","I69244","I69249",
"I69251","I69252","I69253","I69254","I69259","I69261",
"I69262","I69263","I69264","I69265","I69269","I69331",
"I69332","I69333","I69334","I69339","I69341","I69342",
"I69343","I69344","I69349","I69351","I69352","I69353",
"I69354","I69359","I69361","I69362","I69363","I69364",
"I69365","I69369","I69831","I69832","I69833","I69834",
"I69839","I69841","I69842","I69843","I69844","I69849",
"I69851","I69852","I69853","I69854","I69859","I69861",
"I69862","I69863","I69864","I69865","I69869","I69931",
"I69932","I69933","I69934","I69939","I69941","I69942",
"I69943","I69944","I69949","I69951","I69952","I69953",
"I69954","I69959","I69961","I69962","I69963","I69964",
"I69965","I69969","R532")
neuro10beta <- c("E7500","E7501","E7502","E7509","E7510","E7511","E7519",
"E7523","E7525","E7526","E7529","E754","F842","G10","G110",
"G111","G112","G113","G114","G118","G119","G120","G121",
"G1220","G1221","G1222","G1223","G1224","G1225","G1229",
"G128","G129","G132","G138","G20","G214","G2401","G2402",
"G2409","G242","G248","G254","G255","G2581","G300","G301",
"G308","G309","G3101","G3109","G311","G312","G3181","G3182",
"G3183","G3184","G3185","G3189","G319","G3281","G35","G361",
"G368","G369","G370","G371","G372","G373","G374","G375","G378",
"G379","G40001","G40009","G40011","G40019","G40101","G40109",
"G40111","G40119","G40201","G40209","G40211","G40219","G40301",
"G40309","G40311","G40319","G40401","G40409","G40411","G40419",
"G40501","G40509","G40801","G40802","G40803","G40804","G40811",
"G40812","G40813","G40814","G40821","G40822","G40823","G40824",
"G4089","G40901","G40909","G40911","G40919","G40A01","G40A09",
"G40A11","G40A19","G40B01","G40B09","G40B11","G40B19","G47411",
"G47419","G47421","G47429","G803","G890","G910","G911","G912",
"G913","G914","G918","G919","G937","G9389","G939","G94","O99350",
"O99351","O99352","O99353","O99354","O99355","P9160","P9161",
"P9162","P9163","R410","R4182","R4701","R5600","R5601","R561","R569")
chronic_pulm10beta <- c("J40","J410","J411","J418","J42","J430","J431",
"J432","J438","J439","J440","J441","J449","J4520",
"J4521","J4522","J4530","J4531","J4532","J4540",
"J4541","J4542","J4550","J4551","J4552","J45901",
"J45902","J45909","J45990","J45991","J45998","J470",
"J471","J479","J60","J61","J620","J628","J630",
"J631","J632","J633","J634","J635","J636","J64",
"J660","J661","J662","J668","J670","J671","J672",
"J673","J674","J675","J676","J677","J678","J679","J684")
diab_uc10beta <- c("E0800","E0801","E0810","E0811","E089","E0900","E0901",
"E0910","E0911","E099","E1010","E1011","E109","E1100",
"E1101","E1110","E1111","E119","E1300","E1301","E1310",
"E1311","E139","O24011","O24012","O24013","O24019",
"O2402","O2403","O24111","O24112","O24113","O24119",
"O2412","O2413","O24311","O24312","O24313","O24319",
"O2432","O2433","O24811","O24812","O24813","O24819",
"O2482","O2483","O24911","O24912","O24913","O24919",
"O2492","O2493")
diab_c10beta <- c("E0821","E0822","E0829","E08311","E08319","E08321",
"E083211","E083212","E083213","E083219","E08329","E083291",
"E083292","E083293","E083299","E08331","E083311","E083312",
"E083313","E083319","E08339","E083391","E083392","E083393",
"E083399","E08341","E083411","E083412","E083413","E083419",
"E08349","E083491","E083492","E083493","E083499","E08351",
"E083511","E083512","E083513","E083519","E083521","E083522",
"E083523","E083529","E083531","E083532","E083533","E083539",
"E083541","E083542","E083543","E083549","E083551","E083552",
"E083553","E083559","E08359","E083591","E083592","E083593",
"E083599","E0836","E0837X1","E0837X2","E0837X3","E0837X9",
"E0839","E0840","E0841","E0842","E0843","E0844","E0849",
"E0851","E0852","E0859","E08610","E08618","E08620","E08621",
"E08622","E08628","E08630","E08638","E08641","E08649","E0865",
"E0869","E088","E0921","E0922","E0929","E09311","E09319",
"E09321","E093211","E093212","E093213","E093219","E09329",
"E093291","E093292","E093293","E093299","E09331","E093311",
"E093312","E093313","E093319","E09339","E093391","E093392",
"E093393","E093399","E09341","E093411","E093412","E093413",
"E093419","E09349","E093491","E093492","E093493","E093499",
"E09351","E093511","E093512","E093513","E093519","E093521",
"E093522","E093523","E093529","E093531","E093532","E093533",
"E093539","E093541","E093542","E093543","E093549","E093551",
"E093552","E093553","E093559","E09359","E093591","E093592",
"E093593","E093599","E0936","E0937X1","E0937X2","E0937X3",
"E0937X9","E0939","E0940","E0941","E0942","E0943","E0944",
"E0949","E0951","E0952","E0959","E09610","E09618","E09620",
"E09621","E09622","E09628","E09630","E09638","E09641","E09649",
"E0965","E0969","E098","E1021","E1022","E1029","E10311",
"E10319","E10321","E103211","E103212","E103213","E103219",
"E10329","E103291","E103292","E103293","E103299","E10331",
"E103311","E103312","E103313","E103319","E10339","E103391",
"E103392","E103393","E103399","E10341","E103411","E103412",
"E103413","E103419","E10349","E103491","E103492","E103493",
"E103499","E10351","E103511","E103512","E103513","E103519",
"E103521","E103522","E103523","E103529","E103531","E103532",
"E103533","E103539","E103541","E103542","E103543","E103549",
"E103551","E103552","E103553","E103559","E10359","E103591",
"E103592","E103593","E103599","E1036","E1037X1","E1037X2",
"E1037X3","E1037X9","E1039","E1040","E1041","E1042","E1043",
"E1044","E1049","E1051","E1052","E1059","E10610","E10618",
"E10620","E10621","E10622","E10628","E10630","E10638","E10641",
"E10649","E1065","E1069","E108","E1121","E1122","E1129",
"E11311","E11319","E11321","E113211","E113212","E113213",
"E113219","E11329","E113291","E113292","E113293","E113299",
"E11331","E113311","E113312","E113313","E113319","E11339",
"E113391","E113392","E113393","E113399","E11341","E113411",
"E113412","E113413","E113419","E11349","E113491","E113492",
"E113493","E113499","E11351","E113511","E113512","E113513",
"E113519","E113521","E113522","E113523","E113529","E113531",
"E113532","E113533","E113539","E113541","E113542","E113543",
"E113549","E113551","E113552","E113553","E113559","E11359",
"E113591","E113592","E113593","E113599","E1136","E1137X1",
"E1137X2","E1137X3","E1137X9","E1139","E1140","E1141","E1142",
"E1143","E1144","E1149","E1151","E1152","E1159","E11610",
"E11618","E11620","E11621","E11622","E11628","E11630",
"E11638","E11641","E11649","E1165","E1169","E118","E1321",
"E1322","E1329","E13311","E13319","E13321","E133211","E133212",
"E133213","E133219","E13329","E133291","E133292","E133293",
"E133299","E13331","E133311","E133312","E133313","E133319",
"E13339","E133391","E133392","E133393","E133399","E13341",
"E133411","E133412","E133413","E133419","E13349","E133491",
"E133492","E133493","E133499","E13351","E133511","E133512",
"E133513","E133519","E133521","E133522","E133523","E133529",
"E133531","E133532","E133533","E133539","E133541","E133542",
"E133543","E133549","E133551","E133552","E133553","E133559",
"E13359","E133591","E133592","E133593","E133599","E1336",
"E1337X1","E1337X2","E1337X3","E1337X9","E1339","E1340",
"E1341","E1342","E1343","E1344","E1349","E1351","E1352",
"E1359","E13610","E13618","E13620","E13621","E13622","E13628",
"E13630","E13638","E13641","E13649","E1365","E1369","E138","P702")
hypo10beta <- c("E000","E001","E002","E009","E018","E02","E030","E031","E032",
"E033","E038","E039","E890")
renal10beta <- c("N183","N184","N185","N186","N189","N19","Z4901","Z4902",
"Z4931","Z4932","Z9115","Z940","Z992",
"I120") #hrnwrf
liver10beta <- c("B180","B181","B182","I8500","I8501","I8510","I8511",
"K700","K702","K7030","K7031","K7040","K7041","K709","
K7210","K7211","K7290","K7291","K730","K731","K732",
"K738","K739","K740","K741","K742","K743","K744","K745",
"K7460","K7469","K754","K7581","K760","K766","K7689","K769",
"Z944")
peptic10beta <- c("K254","K255","K256","K257","K259","K264","K265","K266",
"K267","K269","K274","K275","K276","K277","K279","K284",
"K285","K286","K287","K289")
hiv10beta <- c("B20")
lymph10beta <- c("C8100","C8101","C8102","C8103","C8104","C8105","C8106",
"C8107","C8108","C8109","C8110","C8111","C8112","C8113",
"C8114","C8115","C8116","C8117","C8118","C8119","C8120",
"C8121","C8122","C8123","C8124","C8125","C8126","C8127",
"C8128","C8129","C8130","C8131","C8132","C8133","C8134",
"C8135","C8136","C8137","C8138","C8139","C8140","C8141",
"C8142","C8143","C8144","C8145","C8146","C8147","C8148",
"C8149","C8170","C8171","C8172","C8173","C8174","C8175",
"C8176","C8177","C8178","C8179","C8190","C8191","C8192",
"C8193","C8194","C8195","C8196","C8197","C8198","C8199",
"C8200","C8201","C8202","C8203","C8204","C8205","C8206",
"C8207","C8208","C8209","C8210","C8211","C8212","C8213",
"C8214","C8215","C8216","C8217","C8218","C8219","C8220",
"C8221","C8222","C8223","C8224","C8225","C8226","C8227",
"C8228","C8229","C8230","C8231","C8232","C8233","C8234",
"C8235","C8236","C8237","C8238","C8239","C8240","C8241",
"C8242","C8243","C8244","C8245","C8246","C8247","C8248",
"C8249","C8250","C8251","C8252","C8253","C8254","C8255",
"C8256","C8257","C8258","C8259","C8260","C8261","C8262",
"C8263","C8264","C8265","C8266","C8267","C8268","C8269",
"C8280","C8281","C8282","C8283","C8284","C8285","C8286",
"C8287","C8288","C8289","C8290","C8291","C8292","C8293",
"C8294","C8295","C8296","C8297","C8298","C8299","C8300",
"C8301","C8302","C8303","C8304","C8305","C8306","C8307",
"C8308","C8309","C8310","C8311","C8312","C8313","C8314",
"C8315","C8316","C8317","C8318","C8319","C8330","C8331",
"C8332","C8333","C8334","C8335","C8336","C8337","C8338",
"C8339","C8350","C8351","C8352","C8353","C8354","C8355",
"C8356","C8357","C8358","C8359","C8370","C8371","C8372",
"C8373","C8374","C8375","C8376","C8377","C8378","C8379",
"C8380","C8381","C8382","C8383","C8384","C8385","C8386",
"C8387","C8388","C8389","C8390","C8391","C8392","C8393",
"C8394","C8395","C8396","C8397","C8398","C8399","C8400",
"C8401","C8402","C8403","C8404","C8405","C8406","C8407",
"C8408","C8409","C8410","C8411","C8412","C8413","C8414",
"C8415","C8416","C8417","C8418","C8419","C8440","C8441",
"C8442","C8443","C8444","C8445","C8446","C8447","C8448",
"C8449","C8460","C8461","C8462","C8463","C8464","C8465",
"C8466","C8467","C8468","C8469","C8470","C8471","C8472",
"C8473","C8474","C8475","C8476","C8477","C8478","C8479",
"C8490","C8491","C8492","C8493","C8494","C8495","C8496",
"C8497","C8498","C8499","C84A0","C84A1","C84A2","C84A3",
"C84A4","C84A5","C84A6","C84A7","C84A8","C84A9","C84Z0",
"C84Z1","C84Z2","C84Z3","C84Z4","C84Z5","C84Z6","C84Z7",
"C84Z8","C84Z9","C8510","C8511","C8512","C8513","C8514",
"C8515","C8516","C8517","C8518","C8519","C8520","C8521",
"C8522","C8523","C8524","C8525","C8526","C8527","C8528",
"C8529","C8580","C8581","C8582","C8583","C8584","C8585",
"C8586","C8587","C8588","C8589","C8590","C8591","C8592",
"C8593","C8594","C8595","C8596","C8597","C8598","C8599",
"C860","C861","C862","C863","C864","C865","C866","C880",
"C882","C883","C884","C888","C889","C9000","C9001","C9002",
"C9010","C9011","C9012","C9020","C9021","C9022","C9030",
"C9031","C9032","C960","C962","C9620","C9621","C9622",
"C9629","C964","C969","C96A","C96Z","D47Z9")
mets10beta <- c("C770","C771","C772","C773","C774","C775","C778","C779",
"C7800","C7801","C7802","C781","C782","C7830","C7839","C784",
"C785","C786","C787","C7880","C7889","C7900","C7901","C7902",
"C7910","C7911","C7919","C792","C7931","C7932","C7940","C7949",
"C7951","C7952","C7960","C7961","C7962","C7970","C7971","C7972",
"C7981","C7982","C7989","C799","C7B00","C7B01","C7B02","C7B03",
"C7B04","C7B09","C7B1","C7B8","C800","C801","R180")
tumor10beta <- c("C000","C001","C002","C003","C004","C005","C006","C008",
"C009","C01","C020","C021","C022","C023","C024","C028",
"C029","C030","C031","C039","C040","C041","C048","C049",
"C050","C051","C052","C058","C059","C060","C061","C062",
"C0680","C0689","C069","C07","C080","C081","C089","C090",
"C091","C098","C099","C100","C101","C102","C103","C104",
"C108","C109","C110","C111","C112","C113","C118","C119",
"C12","C130","C131","C132","C138","C139","C140","C142",
"C148","C153","C154","C155","C158","C159","C160","C161",
"C162","C163","C164","C165","C166","C168","C169","C170",
"C171","C172","C173","C178","C179","C180","C181","C182",
"C183","C184","C185","C186","C187","C188","C189","C19",
"C20","C210","C211","C212","C218","C220","C221","C222",
"C223","C224","C227","C228","C229","C23","C240","C241",
"C248","C249","C250","C251","C252","C253","C254","C257",
"C258","C259","C260","C261","C269","C300","C301","C310",
"C311","C312","C313","C318","C319","C320","C321","C322",
"C323","C328","C329","C33","C3400","C3401","C3402","C3410",
"C3411","C3412","C342","C3430","C3431","C3432","C3480",
"C3481","C3482","C3490","C3491","C3492","C37","C380","C381",
"C382","C383","C384","C388","C390","C399","C4000","C4001",
"C4002","C4010","C4011","C4012","C4020","C4021","C4022",
"C4030","C4031","C4032","C4080","C4081","C4082","C4090",
"C4091","C4092","C410","C411","C412","C413","C414","C419",
"C430","C4310","C4311","C43111","C43112","C4312","C43121",
"C43122","C4320","C4321","C4322","C4330","C4331","C4339",
"C434","C4351","C4352","C4359","C4360","C4361","C4362",
"C4370","C4371","C4372","C438","C439","C450","C451","C452",
"C457","C470","C4710","C4711","C4712","C4720","C4721","C4722",
"C473","C474","C475","C476","C478","C479","C480","C481","C482",
"C488","C490","C4910","C4911","C4912","C4920","C4921","C4922",
"C493","C494","C495","C496","C498","C499","C49A0","C49A1",
"C49A2","C49A3","C49A4","C49A5","C49A9","C4A0","C4A10",
"C4A11","C4A111","C4A112","C4A12","C4A121","C4A122",
"C4A20","C4A21","C4A22","C4A30","C4A31","C4A39","C4A4",
"C4A51","C4A52","C4A59","C4A60","C4A61","C4A62","C4A70",
"C4A71","C4A72","C4A8","C4A9","C50011","C50012","C50019",
"C50021","C50022","C50029","C50111","C50112","C50119",
"C50121","C50122","C50129","C50211","C50212","C50219",
"C50221","C50222","C50229","C50311","C50312","C50319",
"C50321","C50322","C50329","C50411","C50412","C50419",
"C50421","C50422","C50429","C50511","C50512","C50519",
"C50521","C50522","C50529","C50611","C50612","C50619",
"C50621","C50622","C50629","C50811","C50812","C50819",
"C50821","C50822","C50829","C50911","C50912","C50919",
"C50921","C50922","C50929","C510","C511","C512","C518",
"C519","C52","C530","C531","C538","C539","C540","C541",
"C542","C543","C548","C549","C55","C561","C562","C569",
"C5700","C5701","C5702","C5710","C5711","C5712","C5720",
"C5721","C5722","C573","C574","C577","C578","C579","C58",
"C600","C601","C602","C608","C609","C61","C6200","C6201",
"C6202","C6210","C6211","C6212","C6290","C6291","C6292",
"C6300","C6301","C6302","C6310","C6311","C6312","C632",
"C637","C638","C639","C641","C642","C649","C651","C652",
"C659","C661","C662","C669","C670","C671","C672","C673",
"C674","C675","C676","C677","C678","C679","C680","C681",
"C688","C689","C6900","C6901","C6902","C6910","C6911",
"C6912","C6920","C6921","C6922","C6930","C6931","C6932",
"C6940","C6941","C6942","C6950","C6951","C6952","C6960",
"C6961","C6962","C6980","C6981","C6982","C6990","C6991",
"C6992","C700","C701","C709","C710","C711","C712","C713",
"C714","C715","C716","C717","C718","C719","C720","C721",
"C7220","C7221","C7222","C7230","C7231","C7232","C7240",
"C7241","C7242","C7250","C7259","C729","C73","C7400",
"C7401","C7402","C7410","C7411","C7412","C7490","C7491",
"C7492","C750","C751","C752","C753","C754","C755","C758",
"C759","C760","C761","C762","C763","C7640","C7641","C7642",
"C7650","C7651","C7652","C768","C7A00","C7A010","C7A011",
"C7A012","C7A019","C7A020","C7A021","C7A022","C7A023",
"C7A024","C7A025","C7A026","C7A029","C7A090","C7A091",
"C7A092","C7A093","C7A094","C7A095","C7A096","C7A098",
"D030","D0310","D0311","D03111","D03112","D0312",
"D03121","D03122","D0320","D0321","D0322","D0330",
"D0339","D034","D0351","D0352","D0359","D0360","D0361",
"D0362","D0370","D0371","D0372","D038","D039","E3121",
"E3122","E3123")
rheum10beta <- c("L900","L940","L941","L943","M0500","M05011","M05012",
"M05019","M05021","M05022","M05029","M05031","M05032",
"M05039","M05041","M05042","M05049","M05051","M05052",
"M05059","M05061","M05062","M05069","M05071","M05072",
"M05079","M0509","M0510","M05111","M05112","M05119",
"M05121","M05122","M05129","M05131","M05132","M05139",
"M05141","M05142","M05149","M05151","M05152","M05159",
"M05161","M05162","M05169","M05171","M05172","M05179",
"M0519","M0520","M05211","M05212","M05219","M05221",
"M05222","M05229","M05231","M05232","M05239","M05241",
"M05242","M05249","M05251","M05252","M05259","M05261",
"M05262","M05269","M05271","M05272","M05279","M0529",
"M0530","M05311","M05312","M05319","M05321","M05322",
"M05329","M05331","M05332","M05339","M05341","M05342",
"M05349","M05351","M05352","M05359","M05361","M05362",
"M05369","M05371","M05372","M05379","M0539","M0540",
"M05411","M05412","M05419","M05421","M05422","M05429",
"M05431","M05432","M05439","M05441","M05442","M05449",
"M05451","M05452","M05459","M05461","M05462","M05469",
"M05471","M05472","M05479","M0549","M0550","M05511",
"M05512","M05519","M05521","M05522","M05529","M05531",
"M05532","M05539","M05541","M05542","M05549","M05551",
"M05552","M05559","M05561","M05562","M05569","M05571",
"M05572","M05579","M0559","M0560","M05611","M05612",
"M05619","M05621","M05622","M05629","M05631","M05632",
"M05639","M05641","M05642","M05649","M05651","M05652",
"M05659","M05661","M05662","M05669","M05671","M05672",
"M05679","M0569","M0570","M05711","M05712","M05719",
"M05721","M05722","M05729","M05731","M05732","M05739",
"M05741","M05742","M05749","M05751","M05752","M05759",
"M05761","M05762","M05769","M05771","M05772","M05779",
"M0579","M0580","M05811","M05812","M05819","M05821",
"M05822","M05829","M05831","M05832","M05839","M05841",
"M05842","M05849","M05851","M05852","M05859","M05861",
"M05862","M05869","M05871","M05872","M05879","M0589",
"M059","M0600","M06011","M06012","M06019","M06021",
"M06022","M06029","M06031","M06032","M06039","M06041",
"M06042","M06049","M06051","M06052","M06059","M06061",
"M06062","M06069","M06071","M06072","M06079","M0608",
"M0609","M061","M0620","M06211","M06212","M06219",
"M06221","M06222","M06229","M06231","M06232","M06239",
"M06241","M06242","M06249","M06251","M06252","M06259",
"M06261","M06262","M06269","M06271","M06272","M06279",
"M0628","M0629","M0630","M06311","M06312","M06319",
"M06321","M06322","M06329","M06331","M06332","M06339",
"M06341","M06342","M06349","M06351","M06352","M06359",
"M06361","M06362","M06369","M06371","M06372","M06379",
"M0638","M0639","M064","M0680","M06811","M06812","M06819",
"M06821","M06822","M06829","M06831","M06832","M06839",
"M06841","M06842","M06849","M06851","M06852","M06859",
"M06861","M06862","M06869","M06871","M06872","M06879",
"M0688","M0689","M069","M0800","M08011","M08012","M08019",
"M08021","M08022","M08029","M08031","M08032","M08039",
"M08041","M08042","M08049","M08051","M08052","M08059",
"M08061","M08062","M08069","M08071","M08072","M08079",
"M0808","M0809","M081","M0820","M08211","M08212","M08219",
"M08221","M08222","M08229","M08231","M08232","M08239",
"M08241","M08242","M08249","M08251","M08252","M08259",
"M08261","M08262","M08269","M08271","M08272","M08279",
"M0828","M0829","M083","M0840","M08411","M08412","M08419",
"M08421","M08422","M08429","M08431","M08432","M08439",
"M08441","M08442","M08449","M08451","M08452","M08459",
"M08461","M08462","M08469","M08471","M08472","M08479",
"M0848","M0880","M08811","M08812","M08819","M08821",
"M08822","M08829","M08831","M08832","M08839","M08841",
"M08842","M08849","M08851","M08852","M08859","M08861",
"M08862","M08869","M08871","M08872","M08879","M0888",
"M0889","M0890","M08911","M08912","M08919","M08921",
"M08922","M08929","M08931","M08932","M08939","M08941",
"M08942","M08949","M08951","M08952","M08959","M08961",
"M08962","M08969","M08971","M08972","M08979","M0898",
"M0899","M1200","M12011","M12012","M12019","M12021",
"M12022","M12029","M12031","M12032","M12039","M12041",
"M12042","M12049","M12051","M12052","M12059","M12061",
"M12062","M12069","M12071","M12072","M12079","M1208",
"M1209","M320","M3210","M3211","M3212","M3213","M3214",
"M3215","M3219","M328","M329","M3300","M3301","M3302",
"M3303","M3309","M3310","M3311","M3312","M3313","M3319",
"M3320","M3321","M3322","M3329","M3390","M3391","M3392",
"M3393","M3399","M340","M341","M342","M3481","M3482","M3483",
"M3489","M349","M3500","M3501","M3502","M3503","M3504",
"M3509","M351","M353","M355","M358","M359","M360","M368",
"M450","M451","M452","M453","M454","M455","M456","M457",
"M458","M459","M4600","M4601","M4602","M4603","M4604",
"M4605","M4606","M4607","M4608","M4609","M461","M4650",
"M4651","M4652","M4653","M4654","M4655","M4656","M4657",
"M4658","M4659","M4680","M4681","M4682","M4683","M4684",
"M4685","M4686","M4687","M4688","M4689","M4690","M4691",
"M4692","M4693","M4694","M4695","M4696","M4697","M4698",
"M4699","M488X1","M488X2","M488X3","M488X4","M488X5",
"M488X6","M488X7","M488X8","M488X9","M4980","M4981",
"M4982","M4983","M4984","M4985","M4986","M4987","M4988",
"M4989")
coag10beta <- c("D65","D66","D67","D680","D681","D682","D68311","D68312",
"D68318","D6832","D684","D688","D689","D691","D693","D6941",
"D6942","D6949","D6951","D6959","D696","D7582","O99111",
"O99112","O99113","O99119","O9912","O9913")
obese10beta <- c("E6601","E6609","E661","E662","E668","E669","O99210",
"O99211","O99212","O99213","O99214","O99215","R939",
"Z6830","Z6831","Z6832","Z6833","Z6834","Z6835","Z6836",
"Z6837","Z6838","Z6839","Z6841","Z6842","Z6843","Z6844",
"Z6845","Z6854")
weightloss10beta <- c("E40","E41","E42","E43","E440","E441","E45","E46",
"E640","R634","R636")
fluid10beta <- c("E860","E861","E869","E870","E871","E872","E873","E874",
"E875","E876","E8770","E8771","E8779","E878")
bld_anem10beta <- c("D500","O9081","O99011","O99012","O99013","O99019",
"O9902","O9903")
def_anem10beta <- c("D501","D508","D509","D510","D511","D512","D513",
"D518","D519","D520","D521","D528","D529","D530",
"D531","D532","D538","D539","D630","D631","D638",
"D649")
alcohol10beta <- c("F1010","F1011","F10120","F10121","F10129","F1014",
"F10150","F10151","F10159","F10180","F10181","F10182",
"F10188","F1019","F1020","F1021","F10220","F10221",
"F10229","F10230","F10231","F10232","F10239","F1024",
"F10250","F10251","F10259","F1026","F1027","F10280",
"F10281","F10282","F10288","F1029","F10921","F1094",
"F10950","F10951","F10959","F1096","F1097","F10980",
"F10981","F10982","F10988","F1099")
drug10beta <- c("F1110","F1111","F11120","F11121","F11122","F11129",
"F1114","F11150","F11151","F11159","F11181","F11182",
"F11188","F1119","F1120","F1121","F11220","F11221",
"F11222","F11229","F1123","F1124","F11250","F11251",
"F11259","F11281","F11282","F11288","F1129","F1210",
"F1211","F12120","F12121","F12122","F12129","F12150",
"F12151","F12159","F12180","F12188","F1219","F1220",
"F1221","F12220","F12221","F12222","F12229","F1223",
"F12250","F12251","F12259","F12280","F12288","F1229",
"F1310","F1311","F13120","F13121","F13129","F1314",
"F13150","F13151","F13159","F13180","F13181","F13182",
"F13188","F1319","F1320","F1321","F13220","F13221",
"F13229","F13230","F13231","F13232","F13239","F1324",
"F13250","F13251","F13259","F1326","F1327","F13280",
"F13281","F13282","F13288","F1329","F1410","F1411",
"F14120","F14121","F14122","F14129","F1414","F14150",
"F14151","F14159","F14180","F14181","F14182","F14188",
"F1419","F1420","F1421","F14220","F14221","F14222",
"F14229","F1423","F1424","F14250","F14251","F14259",
"F14280","F14281","F14282","F14288","F1429","F1510",
"F1511","F15120","F15121","F15122","F15129","F1514",
"F15150","F15151","F15159","F15180","F15181","F15182",
"F15188","F1519","F1520","F1521","F15220","F15221",
"F15222","F15229","F1523","F1524","F15250","F15251",
"F15259","F15280","F15281","F15282","F15288","F1529",
"F1610","F1611","F16120","F16121","F16122","F16129",
"F1614","F16150","F16151","F16159","F16180","F16183",
"F16188","F1619","F1620","F1621","F16220","F16221",
"F16229","F1624","F16250","F16251","F16259","F16280",
"F16283","F16288","F1629","F1810","F1811","F18120",
"F18121","F18129","F1814","F18150","F18151","F18159",
"F1817","F18180","F18188","F1819","F1820","F1821",
"F18220","F18221","F18229","F1824","F18250","F18251",
"F18259","F1827","F18280","F18288","F1829","F1910",
"F1911","F19120","F19121","F19122","F19129","F1914",
"F19150","F19151","F19159","F1916","F1917","F19180",
"F19181","F19182","F19188","F1919","F1920","F1921","F19220",
"F19221","F19222","F19229","F19230","F19231","F19232",
"F19239","F1924","F19250","F19251","F19259","F1926","F1927",
"F19280","F19281","F19282","F19288","F1929","F550","F551",
"F552","F553","F554","F558","O99320","O99321","O99322",
"O99323","O99324","O99325")
psych10beta <- c("F200","F201","F202","F203","F205","F2081","F2089","F209",
"F22","F23","F24","F250","F251","F258","F259","F28","F29",
"F3010","F3011","F3012","F3013","F302","F303","F304","F308",
"F309","F310","F3110","F3111","F3112","F3113","F312","F3130",
"F3131","F3132","F314","F315","F3160","F3161","F3162","F3163",
"F3164","F3170","F3171","F3172","F3173","F3174","F3175",
"F3176","F3177","F3178","F3181","F3189","F319","F324",
"F325","F3340","F3341","F3342","F348","F3481","F3489",
"F349","F39","F4489","F843")
depress10beta <- c("F320","F321","F322","F323","F328","F3281","F3289",
"F329","F330","F331","F332","F333","F338","F339",
"F341","F4321")
# Code -----
dat <- dat %>%
dplyr::filter({{version_var}} == 9 | {{version_var}} == 10)
dat1 <- dat %>%
dplyr::mutate(chf = dplyr::if_else(({{version_var}} == 9 & (dx %in% chf9 )| stringr::str_starts(dx, paste(chf9_str))) |
({{version_var}} == 10 & (dx %in% chf10beta)),
1, 0),
valve = dplyr::if_else(({{version_var}} == 9 & (dx %in% valve9 | stringr::str_starts(dx, paste(valve9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% valve10beta),
1, 0),
pulmcirc = dplyr::if_else(({{version_var}} == 9 & (dx %in% pulmcirc9 | stringr::str_starts(dx, paste(pulmcirc9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% pulmcirc10beta),
1, 0),
periph_vasc = dplyr::if_else(({{version_var}} == 9 & (dx %in% periph_vasc9 | stringr::str_starts(dx, paste(periph_vasc9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% periph_vasc10beta),
1, 0),
htn_uc = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(htn_uc9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% htn_uc10beta),
1, 0),
htn_c = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(htn_c9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% htn_c10beta),
1 ,0),
paralysis = dplyr::if_else(({{version_var}} == 9 & (dx %in% paralysis9 | stringr::str_starts(dx, paste(paralysis9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% paralysis10beta),
1, 0),
neuro = dplyr::if_else(({{version_var}} == 9 & (dx %in% neuro9 | stringr::str_starts(dx, paste(neuro9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% neuro10beta),
1, 0),
chronic_pulm = dplyr::if_else(({{version_var}} == 9 & (dx %in% chronic_pulm9 | stringr::str_starts(dx, paste(chronic_pulm9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% chronic_pulm10beta),
1, 0),
diab_uc = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(diab_uc9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% diab_uc10beta),
1, 0),
diab_c = dplyr::if_else(({{version_var}} == 9 & (dx %in% diab_c9 | stringr::str_starts(dx, paste(diab_c9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% diab_c10beta),
1, 0),
hypo = dplyr::if_else(({{version_var}} == 9 & dx %in% hypo9) |
({{version_var}} == 10 & dx %in% hypo10beta),
1, 0),
renal = dplyr::if_else(({{version_var}} == 9 & (dx %in% renal9 | stringr::str_starts(dx, paste(renal9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% renal10beta),
1, 0),
liver = dplyr::if_else(({{version_var}} == 9 & (dx %in% liver9 | stringr::str_starts(dx, paste(liver9_str)))) |
({{version_var}} == 10 & dx %in% liver10beta),
1, 0),
peptic = dplyr::if_else(({{version_var}} == 9 & dx %in% peptic9) |
({{version_var}} == 10 & dx %in% peptic10beta),
1, 0),
hiv = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(hiv9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% hiv10beta),
1 ,0),
lymph = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(lymph9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% lymph10beta),
1, 0),
mets = dplyr::if_else(({{version_var}} == 9 & (dx %in% mets9 | stringr::str_starts(dx, paste(mets9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% mets10beta),
1, 0),
tumor = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(tumor9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% tumor10beta),
1, 0),
rheum = dplyr::if_else(({{version_var}} == 9 & (dx %in% rheum9 | stringr::str_starts(dx, paste(rheum9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% rheum10beta),
1, 0),
coag = dplyr::if_else(({{version_var}} == 9 & (dx %in% coag9 | stringr::str_starts(dx, paste(coag9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% coag10beta),
1, 0),
obese = dplyr::if_else(({{version_var}} == 9 & (dx %in% obese9 | stringr::str_starts(dx, paste(obese9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% obese10beta),
1, 0),
weightloss = dplyr::if_else(({{version_var}} == 9 & (dx %in% weightloss9 | stringr::str_starts(dx, paste(weightloss9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% weightloss10beta),
1, 0),
fluid = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(fluid9_str))) |
({{version_var}} == 10 & dx %in% fluid10beta),
1, 0),
bld_anem = dplyr::if_else(({{version_var}} == 9 & (dx %in% bld_anem9 | stringr::str_starts(dx, paste(bld_anem9_str)))) |
({{version_var}} == 10 & dx %in% bld_anem10beta),
1, 0),
def_anem = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(def_anem9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% def_anem10beta),
1, 0),
alcohol = dplyr::if_else(({{version_var}} == 9 & (dx %in% alc9 | stringr::str_starts(dx, paste(alcohol9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% alcohol10beta),
1, 0),
drug = dplyr::if_else(({{version_var}} == 9 & (dx %in% drug9 | stringr::str_starts(dx, paste(drug9_str, sep = "|", collapse = "|")))) |
({{version_var}} == 10 & dx %in% drug10beta),
1, 0),
psych = dplyr::if_else(({{version_var}} == 9 & stringr::str_starts(dx, paste(psych9_str, sep = "|", collapse = "|"))) |
({{version_var}} == 10 & dx %in% psych10beta),
1, 0),
depression = dplyr::if_else(({{version_var}} == 9 & dx %in% depress9) |
({{version_var}} == 10 & dx %in% depress10beta),
1, 0))
dat1 <- dat1 %>%
dplyr::mutate(htn_uc = dplyr::if_else(.data$htn_c == 1, 0,.data$htn_uc),
tumor = dplyr::if_else(.data$mets == 1, 0, .data$tumor),
diab_uc = dplyr::if_else(.data$diab_c == 1, 0, .data$diab_uc),
htn_comb = dplyr::if_else(.data$htn_c == 1 | .data$htn_uc == 1, 1, 0))
}
else {stop("Please specify the version (9 = ICD9, 10 = ICD10, or 19 = ICD9 and ICD10) of your diagnoses codes.")
}
# Outpatient Algorithms ----
## No OT Limitation ----
### ICD-9 or Both ----
if (outpatient_two == "no" & (version == 9 | version == 19)){
dat2 <- dplyr::rename(dat1, "id" = id2)
dat2 <- dat2 %>%
dplyr::mutate(elix_chf = .data$chf,
elix_valve = .data$valve,
elix_pulmcirc = .data$pulmcirc,
elix_periph_vasc = .data$periph_vasc,
elix_htn_uc = .data$htn_uc,
elix_htn_c = .data$htn_c,
elix_paralysis = .data$paralysis,
elix_neuro = .data$neuro,
elix_chronic_pulm = .data$chronic_pulm,
elix_diab_uc = .data$diab_uc,
elix_diab_c = .data$diab_c,
elix_hypo = .data$hypo,
elix_renal = .data$renal,
elix_liver = .data$liver,
elix_peptic = .data$peptic,
elix_hiv = .data$hiv,
elix_lymph = .data$lymph,
elix_mets = .data$mets,
elix_tumor = .data$tumor,
elix_rheum = .data$rheum,
elix_coag = .data$coag,
elix_obese = .data$obese,
elix_weightloss = .data$weightloss,
elix_fluid = .data$fluid,
elix_bld_anem = .data$bld_anem,
elix_def_anem = .data$def_anem,
elix_alcohol = .data$alcohol,
elix_drug = .data$drug,
elix_psych = .data$psych,
elix_depression = .data$depression)
dat2 <- dat2 %>%
dplyr::select(id, tidyselect::starts_with("elix"))
}
### ICD_10 ----
else if (outpatient_two == "no" & version == 10){
dat2 <- dplyr::rename(dat1, "id" = id2)
dat2 <- dat2 %>%
dplyr::mutate(elix_aids = .data$aids,
elix_alcohol = .data$alcohol,
elix_def_anem = .data$def_anem,
elix_rheum = .data$rheum,
elix_bld_loss = .data$bld_loss,
elix_cancer_leuk = .data$cancer_leuk,
elix_cancer_lymph = .data$cancer_lymph,
elix_cancer_mets = .data$cancer_mets,
elix_cancer_solid = .data$cancer_solid,
elix_cancer_insitu = .data$cancer_insitu,
elix_cbvd = .data$cbvd,
elix_chf = .data$chf,
elix_coag = .data$coag,
elix_dementia = .data$dementia,
elix_depress = .data$depress,
elix_diab_c = .data$diab_c,
elix_diab_uc = .data$diab_uc,
elix_drug = .data$drug,
elix_htn_c = .data$htn_c,
elix_htn_uc = .data$htn_uc,
elix_liver_mild = .data$liver_mild,
elix_liver_sev = .data$liver_sev,
elix_chronic_pulm = .data$chronic_pulm,
elix_neuro_movt = .data$neuro_movt,
elix_neuro_seiz = .data$neuro_seiz,
elix_neuro_oth = .data$neuro_oth,
elix_obese = .data$obese,
elix_paralysis = .data$paralysis,
elix_perivasc = .data$perivasc,
elix_psych = .data$psych,
elix_pulmcirc = .data$pulmcirc,
elix_renal_mod = .data$renal_mod,
elix_renal_sev = .data$renal_sev,
elix_hypo = .data$hypo,
elix_thyroid_oth = .data$thyroid_oth,
elix_peptic = .data$peptic,
elix_valve = .data$valve,
elix_weightloss = .data$weightloss)
dat2 <- dat2 %>%
dplyr::select(id, tidyselect::starts_with("elix"))
}
## ICD-9 or Both ----
else if ((outpatient_two == "yes" | outpatient_two == "Yes") & (version == 9 | version == 19)){
message("Message: You have specified that for a comorbidity to be positvely coded, an individual must have two outpatient claims with it. Please make sure the levels of your variable denoting outpatient type are either 'ot' or 'OT'")
dat_ot <- dat1 %>%
dplyr::filter(.data$type == "ot" | .data$type == "OT")
dat_ip <- dat1 %>%
dplyr::filter(.data$type != "ot" & .data$type != "OT")
dat_ot_sum <- dat_ot %>%
dplyr::group_by({{id}}) %>%
dplyr::summarize(
chf_ot = sum(.data$chf),
valve_ot = sum(.data$valve),
pulmcirc_ot = sum(.data$pulmcirc),
periph_vasc_ot = sum(.data$periph_vasc),
htn_uc_ot = sum(.data$htn_uc),
htn_c_ot = sum(.data$htn_c),
paralysis_ot = sum(.data$paralysis),
neuro_ot = sum(.data$neuro),
chronic_pulm_ot = sum(.data$chronic_pulm),
diab_uc_ot = sum(.data$diab_uc),
diab_c_ot = sum(.data$diab_c),
hypo_ot = sum(.data$hypo),
renal_ot = sum(.data$renal),
liver_ot = sum(.data$liver),
peptic_ot = sum(.data$peptic),
hiv_ot = sum(.data$hiv),
lymph_ot = sum(.data$lymph),
mets_ot = sum(.data$mets),
tumor_ot = sum(.data$tumor),
rheum_ot = sum(.data$rheum),
coag_ot = sum(.data$coag),
obese_ot = sum(.data$obese),
weightloss_ot = sum(.data$weightloss),
fluid_ot = sum(.data$fluid),
bld_anem_ot = sum(.data$bld_anem),
def_anem_ot = sum(.data$def_anem),
alcohol_ot = sum(.data$alcohol),
drug_ot = sum(.data$drug),
psych_ot = sum(.data$psych),
depression_ot = sum(.data$depression)) %>%
dplyr::ungroup()
dat_ip_sum <- dat_ip %>%
dplyr::group_by({{id}}) %>%
dplyr::summarize(
chf_ip = max(.data$chf),
valve_ip = max(.data$valve),
pulmcirc_ip = max(.data$pulmcirc),
periph_vasc_ip = max(.data$periph_vasc),
htn_uc_ip = max(.data$htn_uc),
htn_c_ip = max(.data$htn_c),
paralysis_ip = max(.data$paralysis),
neuro_ip = max(.data$neuro),
chronic_pulm_ip = max(.data$chronic_pulm),
diab_uc_ip = max(.data$diab_uc),
diab_c_ip = max(.data$diab_c),
hypo_ip = max(.data$hypo),
renal_ip = max(.data$renal),
liver_ip = max(.data$liver),
peptic_ip = max(.data$peptic),
hiv_ip = max(.data$hiv),
lymph_ip = max(.data$lymph),
mets_ip = max(.data$mets),
tumor_ip = max(.data$tumor),
rheum_ip = max(.data$rheum),
coag_ip = max(.data$coag),
obese_ip = max(.data$obese),
weightloss_ip = max(.data$weightloss),
fluid_ip = max(.data$fluid),
bld_anem_ip = max(.data$bld_anem),
def_anem_ip = max(.data$def_anem),
alcohol_ip = max(.data$alcohol),
drug_ip = max(.data$drug),
psych_ip = max(.data$psych),
depression_ip = max(.data$depression)) %>%
dplyr::ungroup()
dat_ip_sum <- dplyr::rename(dat_ip_sum, "id" = id2)
dat_ot_sum <- dplyr::rename(dat_ot_sum, "id" = id2)
dat_comb <- dplyr::full_join(dat_ip_sum, dat_ot_sum, by = "id")
dat_comb <- dat_comb %>%
dplyr::mutate(elix_chf = dplyr::if_else(.data$chf_ot >= 2 | .data$chf_ip >=1, 1, 0, missing = 0),
elix_valve = dplyr::if_else(.data$valve_ot >= 2 | .data$valve_ip >=1, 1, 0, missing = 0),
elix_pulmcirc = dplyr::if_else(.data$pulmcirc_ot >= 2 | .data$pulmcirc_ip >=1, 1, 0, missing = 0),
elix_periph_vasc = dplyr::if_else(.data$periph_vasc_ot >= 2 | .data$periph_vasc_ip >=1, 1, 0, missing = 0),
elix_htn_uc = dplyr::if_else(.data$htn_uc_ot >= 2 | .data$htn_uc_ip >=1, 1, 0, missing = 0),
elix_htn_c = dplyr::if_else(.data$htn_c_ot >= 2 | .data$htn_c_ip >=1, 1, 0, missing = 0),
elix_paralysis = dplyr::if_else(.data$paralysis_ot >= 2 | .data$paralysis_ip >=1, 1, 0, missing = 0),
elix_neuro = dplyr::if_else(.data$neuro_ot >= 2 | .data$neuro_ip >=1, 1, 0, missing = 0),
elix_chronic_pulm = dplyr::if_else(.data$chronic_pulm_ot >= 2 | .data$chronic_pulm_ip >=1, 1, 0, missing = 0),
elix_diab_uc = dplyr::if_else(.data$diab_uc_ot >= 2 | .data$diab_uc_ip >=1, 1, 0, missing = 0),
elix_diab_c = dplyr::if_else(.data$diab_c_ot >= 2 | .data$diab_c_ip >=1, 1, 0, missing = 0),
elix_hypo = dplyr::if_else(.data$hypo_ot >= 2 | .data$hypo_ip >=1, 1, 0, missing = 0),
elix_renal = dplyr::if_else(.data$renal_ot >= 2 | .data$renal_ip >=1, 1, 0, missing = 0),
elix_liver = dplyr::if_else(.data$liver_ot >= 2 | .data$liver_ip >=1, 1, 0, missing = 0),
elix_peptic = dplyr::if_else(.data$peptic_ot >= 2 | .data$peptic_ip >=1, 1, 0, missing = 0),
elix_hiv = dplyr::if_else(.data$hiv_ot >= 2 | .data$hiv_ip >=1, 1, 0, missing = 0),
elix_lymph = dplyr::if_else(.data$lymph_ot >= 2 | .data$lymph_ip >=1, 1, 0, missing = 0),
elix_mets = dplyr::if_else(.data$mets_ot >= 2 | .data$mets_ip >=1, 1, 0, missing = 0),
elix_tumor = dplyr::if_else(.data$tumor_ot >= 2 | .data$tumor_ip >=1, 1, 0, missing = 0),
elix_rheum = dplyr::if_else(.data$rheum_ot >= 2 | .data$rheum_ip >=1, 1, 0, missing = 0),
elix_coag = dplyr::if_else(.data$coag_ot >= 2 | .data$coag_ip >=1, 1, 0, missing = 0),
elix_obese = dplyr::if_else(.data$obese_ot >= 2 | .data$obese_ip >=1, 1, 0, missing = 0),
elix_weightloss = dplyr::if_else(.data$weightloss_ot >= 2 | .data$weightloss_ip >=1, 1, 0, missing = 0),
elix_fluid = dplyr::if_else(.data$fluid_ot >= 2 | .data$fluid_ip >=1, 1, 0, missing = 0),
elix_bld_anem = dplyr::if_else(.data$bld_anem_ot >= 2 | .data$bld_anem_ip >=1, 1, 0, missing = 0),
elix_def_anem = dplyr::if_else(.data$def_anem_ot >= 2 | .data$def_anem_ip >=1, 1, 0, missing = 0),
elix_alcohol = dplyr::if_else(.data$alcohol_ot >= 2 | .data$alcohol_ip >=1, 1, 0, missing = 0),
elix_drug = dplyr::if_else(.data$drug_ot >= 2 | .data$drug_ip >=1, 1, 0, missing = 0),
elix_psych = dplyr::if_else(.data$psych_ot >= 2 | .data$psych_ip >=1, 1, 0, missing = 0),
elix_depression = dplyr::if_else(.data$depression_ot >= 2 | .data$depression_ip >=1, 1, 0, missing = 0))
dat2 <- dat_comb %>%
dplyr::select(id, tidyselect::starts_with("elix"))
}
## ICD-10 ----
else if(outpatient_two == "yes" | outpatient_two == "Yes"){
message("Message: You have specified that for a comorbidity to be positvely coded, an individual must have two outpatient claims with it. Please make sure the levels of your variable denoting outpatient type must be either 'ot' or 'OT'")
dat_ot <- dat1 %>%
dplyr::filter(.data$type == "ot" | .data$type == "OT")
dat_ip <- dat1 %>%
dplyr::filter(.data$type != "ot" & .data$type != "OT")
dat_ot_sum <- dat_ot %>%
dplyr::group_by({{id}}) %>%
dplyr::summarize(
aids_ot = sum(.data$aids),
alcohol_ot = sum(.data$alcohol),
def_anem_ot = sum(.data$def_anem),
rheum_ot = sum(.data$rheum),
bld_loss_ot = sum(.data$bld_loss),
cancer_leuk_ot = sum(.data$cancer_leuk),
cancer_lymph_ot = sum(.data$cancer_lymph),
cancer_mets_ot = sum(.data$cancer_mets),
cancer_solid_ot = sum(.data$cancer_solid),
cancer_insitu_ot = sum(.data$cancer_insitu),
cbvd_ot = sum(.data$cbvd),
chf_ot = sum(.data$chf),
coag_ot = sum(.data$coag),
dementia_ot = sum(.data$dementia),
depress_ot = sum(.data$depress),
diab_c_ot = sum(.data$diab_c),
diab_uc_ot = sum(.data$diab_uc),
drug_ot = sum(.data$drug),
htn_c_ot = sum(.data$htn_c),
htn_uc_ot = sum(.data$htn_uc),
liver_mild_ot = sum(.data$liver_mild),
liver_sev_ot = sum(.data$liver_sev),
chronic_pulm_ot = sum(.data$chronic_pulm),
neuro_movt_ot = sum(.data$neuro_movt),
neuro_seiz_ot = sum(.data$neuro_seiz),
neuro_oth_ot = sum(.data$neuro_oth),
obese_ot = sum(.data$obese),
paralysis_ot = sum(.data$paralysis),
perivasc_ot = sum(.data$perivasc),
psych_ot = sum(.data$psych),
pulmcirc_ot = sum(.data$pulmcirc),
renal_mod_ot = sum(.data$renal_mod),
renal_sev_ot = sum(.data$renal_sev),
hypo_ot = sum(.data$hypo),
thyroid_oth_ot = sum(.data$thyroid_oth),
peptic_ot = sum(.data$peptic),
valve_ot = sum(.data$valve),
weightloss_ot = sum(.data$weightloss)) %>%
dplyr::ungroup()
dat_ip_sum <- dat_ip %>%
dplyr::group_by({{id}}) %>%
dplyr::summarize(
aids_ip = max(.data$aids),
alcohol_ip = max(.data$alcohol),
def_anem_ip = max(.data$def_anem),
rheum_ip = max(.data$rheum),
bld_loss_ip = max(.data$bld_loss),
cancer_leuk_ip = max(.data$cancer_leuk),
cancer_lymph_ip = max(.data$cancer_lymph),
cancer_mets_ip = max(.data$cancer_mets),
cancer_solid_ip = max(.data$cancer_solid),
cancer_insitu_ip = max(.data$cancer_insitu),
cbvd_ip = max(.data$cbvd),
chf_ip = max(.data$chf),
coag_ip = max(.data$coag),
dementia_ip = max(.data$dementia),
depress_ip = max(.data$depress),
diab_c_ip = max(.data$diab_c),
diab_uc_ip = max(.data$diab_uc),
drug_ip = max(.data$drug),
htn_c_ip = max(.data$htn_c),
htn_uc_ip = max(.data$htn_uc),
liver_mild_ip = max(.data$liver_mild),
liver_sev_ip = max(.data$liver_sev),
chronic_pulm_ip = max(.data$chronic_pulm),
neuro_movt_ip = max(.data$neuro_movt),
neuro_seiz_ip = max(.data$neuro_seiz),
neuro_oth_ip = max(.data$neuro_oth),
obese_ip = max(.data$obese),
paralysis_ip = max(.data$paralysis),
perivasc_ip = max(.data$perivasc),
psych_ip = max(.data$psych),
pulmcirc_ip = max(.data$pulmcirc),
renal_mod_ip = max(.data$renal_mod),
renal_sev_ip = max(.data$renal_sev),
hypo_ip = max(.data$hypo),
thyroid_oth_ip = max(.data$thyroid_oth),
peptic_ip = max(.data$peptic),
valve_ip = max(.data$valve),
weightloss_ip = max(.data$weightloss)) %>%
dplyr::ungroup()
dat_ip_sum <- dplyr::rename(dat_ip_sum, "id" = id2)
dat_ot_sum <- dplyr::rename(dat_ot_sum, "id" = id2)
dat_comb <- dplyr::full_join(dat_ip_sum, dat_ot_sum, by = "id")
dat_comb <- dat_comb %>%
dplyr::mutate(elix_aids = dplyr::if_else(.data$aids_ot >= 2 | .data$aids_ip >= 1, 1, 0, missing = 0),
elix_alcohol = dplyr::if_else(.data$alcohol_ot >= 2 | .data$alcohol_ip >= 1, 1, 0, missing = 0),
elix_def_anem = dplyr::if_else(.data$def_anem_ot >= 2 | .data$def_anem_ip >= 1, 1, 0, missing = 0),
elix_rheum = dplyr::if_else(.data$rheum_ot >= 2 | .data$rheum_ip >= 1, 1, 0, missing = 0),
elix_bld_loss = dplyr::if_else(.data$bld_loss_ot >= 2 | .data$bld_loss_ip >= 1, 1, 0, missing = 0),
elix_cancer_leuk = dplyr::if_else(.data$cancer_leuk_ot >= 2 | .data$cancer_leuk_ip >= 1, 1, 0, missing = 0),
elix_cancer_lymph = dplyr::if_else(.data$cancer_lymph_ot >= 2 | .data$cancer_lymph_ip >= 1, 1, 0, missing = 0),
elix_cancer_mets = dplyr::if_else(.data$cancer_mets_ot >= 2 | .data$cancer_mets_ip >= 1, 1, 0, missing = 0),
elix_cancer_solid = dplyr::if_else(.data$cancer_solid_ot >= 2 | .data$cancer_solid_ip >= 1, 1, 0, missing = 0),
elix_cancer_insitu = dplyr::if_else(.data$cancer_insitu_ot >= 2 | .data$cancer_insitu_ip >= 1, 1, 0, missing = 0),
elix_cbvd = dplyr::if_else(.data$cbvd_ot >= 2 | .data$cbvd_ip >= 1, 1, 0, missing = 0),
elix_chf = dplyr::if_else(.data$chf_ot >= 2 | .data$chf_ip >= 1, 1, 0, missing = 0),
elix_coag = dplyr::if_else(.data$coag_ot >= 2 | .data$coag_ip >= 1, 1, 0, missing = 0),
elix_dementia = dplyr::if_else(.data$dementia_ot >= 2 | .data$dementia_ip >= 1, 1, 0, missing = 0),
elix_depress = dplyr::if_else(.data$depress_ot >= 2 | .data$depress_ip >= 1, 1, 0, missing = 0),
elix_diab_c = dplyr::if_else(.data$diab_c_ot >= 2 | .data$diab_c_ip >= 1, 1, 0, missing = 0),
elix_diab_uc = dplyr::if_else(.data$diab_uc_ot >= 2 | .data$diab_uc_ip >= 1, 1, 0, missing = 0),
elix_drug = dplyr::if_else(.data$drug_ot >= 2 | .data$drug_ip >= 1, 1, 0, missing = 0),
elix_htn_c = dplyr::if_else(.data$htn_c_ot >= 2 | .data$htn_c_ip >= 1, 1, 0, missing = 0),
elix_htn_uc = dplyr::if_else(.data$htn_uc_ot >= 2 | .data$htn_uc_ip >= 1, 1, 0, missing = 0),
elix_liver_mild = dplyr::if_else(.data$liver_mild_ot >= 2 | .data$liver_mild_ip >= 1, 1, 0, missing = 0),
elix_liver_sev = dplyr::if_else(.data$liver_sev_ot >= 2 | .data$liver_sev_ip >= 1, 1, 0, missing = 0),
elix_chronic_pulm = dplyr::if_else(.data$chronic_pulm_ot >= 2 | .data$chronic_pulm_ip >= 1, 1, 0, missing = 0),
elix_neuro_movt = dplyr::if_else(.data$neuro_movt_ot >= 2 | .data$neuro_movt_ip >= 1, 1, 0, missing = 0),
elix_neuro_seiz = dplyr::if_else(.data$neuro_seiz_ot >= 2 | .data$neuro_seiz_ip >= 1, 1, 0, missing = 0),
elix_neuro_oth = dplyr::if_else(.data$neuro_oth_ot >= 2 | .data$neuro_oth_ip >= 1, 1, 0, missing = 0),
elix_obese = dplyr::if_else(.data$obese_ot >= 2 | .data$obese_ip >= 1, 1, 0, missing = 0),
elix_paralysis = dplyr::if_else(.data$paralysis_ot >= 2 | .data$paralysis_ip >= 1, 1, 0, missing = 0),
elix_perivasc = dplyr::if_else(.data$perivasc_ot >= 2 | .data$perivasc_ip >= 1, 1, 0, missing = 0),
elix_psych = dplyr::if_else(.data$psych_ot >= 2 | .data$psych_ip >= 1, 1, 0, missing = 0),
elix_pulmcirc = dplyr::if_else(.data$pulmcirc_ot >= 2 | .data$pulmcirc_ip >= 1, 1, 0, missing = 0),
elix_renal_mod = dplyr::if_else(.data$renal_mod_ot >= 2 | .data$renal_mod_ip >= 1, 1, 0, missing = 0),
elix_renal_sev = dplyr::if_else(.data$renal_sev_ot >= 2 | .data$renal_sev_ip >= 1, 1, 0, missing = 0),
elix_hypo = dplyr::if_else(.data$hypo_ot >= 2 | .data$hypo_ip >= 1, 1, 0, missing = 0),
elix_thyroid_oth = dplyr::if_else(.data$thyroid_oth_ot >= 2 | .data$thyroid_oth_ip >= 1, 1, 0, missing = 0),
elix_peptic = dplyr::if_else(.data$peptic_ot >= 2 | .data$peptic_ip >= 1, 1, 0, missing = 0),
elix_valve = dplyr::if_else(.data$valve_ot >= 2 | .data$valve_ip >= 1, 1, 0, missing = 0),
elix_weightloss = dplyr::if_else(.data$weightloss_ot >= 2 | .data$weightloss_ip >= 1, 1, 0, missing = 0))
dat2 <- dat_comb %>%
dplyr::select(id, tidyselect::starts_with("elix"))
}
# Final Summary ----
if (version == 9 | version == 19){
dat3 <- dat2 %>%
dplyr::group_by(id) %>%
dplyr::summarize(
elix_chf = max(.data$elix_chf),
elix_valve = max(.data$elix_valve),
elix_pulmcirc = max(.data$elix_pulmcirc),
elix_periph_vasc = max(.data$elix_periph_vasc),
elix_htn_uc = max(.data$elix_htn_uc),
elix_htn_c = max(.data$elix_htn_c),
elix_paralysis = max(.data$elix_paralysis),
elix_neuro = max(.data$elix_neuro),
elix_chronic_pulm = max(.data$elix_chronic_pulm),
elix_diab_uc = max(.data$elix_diab_uc),
elix_diab_c = max(.data$elix_diab_c),
elix_hypo = max(.data$elix_hypo),
elix_renal = max(.data$elix_renal),
elix_liver = max(.data$elix_liver),
elix_peptic = max(.data$elix_peptic),
elix_hiv = max(.data$elix_hiv),
elix_lymph = max(.data$elix_lymph),
elix_mets = max(.data$elix_mets),
elix_tumor = max(.data$elix_tumor),
elix_rheum = max(.data$elix_rheum),
elix_coag = max(.data$elix_coag),
elix_obese = max(.data$elix_obese),
elix_weightloss = max(.data$elix_weightloss),
elix_fluid = max(.data$elix_fluid),
elix_bld_anem = max(.data$elix_bld_anem),
elix_def_anem = max(.data$elix_def_anem),
elix_alcohol = max(.data$elix_alcohol),
elix_drug = max(.data$elix_drug),
elix_psych = max(.data$elix_psych),
elix_depression = max(.data$elix_depression)) %>%
dplyr::ungroup()
dat3 <- dat3 %>%
dplyr::mutate(elix_htn_comb = dplyr::if_else(.data$elix_htn_uc == 1 | .data$elix_htn_c == 1, 1, 0))
dat3 <- dat3 %>%
dplyr::mutate(elix_death = .data$elix_hiv*0 + .data$elix_alcohol*-1 + .data$elix_def_anem*-2 + .data$elix_rheum*0 +
.data$elix_bld_anem*-3 + .data$elix_chf*9 + .data$elix_chronic_pulm*3 + .data$elix_coag*11 +
.data$elix_depression*-5 + .data$elix_diab_uc*0 + .data$elix_diab_c*-3 + .data$elix_drug*-7 +
.data$elix_htn_comb*-1 + .data$elix_hypo*0 + .data$elix_liver*4 + .data$elix_lymph*6 + .data$elix_fluid*11 +
.data$elix_mets*14 + .data$elix_neuro*5 + .data$elix_obese*-5 + .data$elix_paralysis*5 + .data$elix_periph_vasc*3 +
.data$elix_psych*-5 + .data$elix_pulmcirc*6 + .data$elix_renal*6 + .data$elix_tumor*7 + .data$elix_peptic*0 + .data$elix_valve*0 +
.data$elix_weightloss*9,
elix_readmit = .data$elix_hiv*19 + .data$elix_alcohol*6 + .data$elix_def_anem*9 + .data$elix_rheum*4 +
.data$elix_bld_anem*3 + .data$elix_chf*13 + .data$elix_chronic_pulm*8 + .data$elix_coag*7 +
.data$elix_depression*4 + .data$elix_diab_uc*6 + .data$elix_diab_c*9 + .data$elix_drug*14 +
.data$elix_htn_comb*-1 + .data$elix_hypo*0 + .data$elix_liver*10 + .data$elix_lymph*16 + .data$elix_fluid*8 +
.data$elix_mets*21 + .data$elix_neuro*7 + .data$elix_obese*-3 + .data$elix_paralysis*6 + .data$elix_periph_vasc*4 +
.data$elix_psych*10 + .data$elix_pulmcirc*5 + .data$elix_renal*15 + .data$elix_tumor*15 + .data$elix_peptic*0 + .data$elix_valve*0 +
.data$elix_weightloss*10)
}
else{
dat3 <- dat2 %>%
dplyr::group_by(id) %>%
dplyr::summarize(
elix_aids = max(.data$elix_aids),
elix_alcohol = max(.data$elix_alcohol),
elix_def_anem = max(.data$elix_def_anem),
elix_rheum = max(.data$elix_rheum),
elix_bld_loss = max(.data$elix_bld_loss),
elix_cancer_leuk = max(.data$elix_cancer_leuk),
elix_cancer_lymph = max(.data$elix_cancer_lymph),
elix_cancer_mets = max(.data$elix_cancer_mets),
elix_cancer_solid = max(.data$elix_cancer_solid),
elix_cancer_insitu = max(.data$elix_cancer_insitu),
elix_cbvd = max(.data$elix_cbvd),
elix_chf = max(.data$elix_chf),
elix_coag = max(.data$elix_coag),
elix_dementia = max(.data$elix_dementia),
elix_depress = max(.data$elix_depress),
elix_diab_c = max(.data$elix_diab_c),
elix_diab_uc = max(.data$elix_diab_uc),
elix_drug = max(.data$elix_drug),
elix_htn_c = max(.data$elix_htn_c),
elix_htn_uc = max(.data$elix_htn_uc),
elix_liver_mild = max(.data$elix_liver_mild),
elix_liver_sev = max(.data$elix_liver_sev),
elix_chronic_pulm = max(.data$elix_chronic_pulm),
elix_neuro_movt = max(.data$elix_neuro_movt),
elix_neuro_seiz = max(.data$elix_neuro_seiz),
elix_neuro_oth = max(.data$elix_neuro_oth),
elix_obese = max(.data$elix_obese),
elix_paralysis = max(.data$elix_paralysis),
elix_perivasc = max(.data$elix_perivasc),
elix_psych = max(.data$elix_psych),
elix_pulmcirc = max(.data$elix_pulmcirc),
elix_renal_mod = max(.data$elix_renal_mod),
elix_renal_sev = max(.data$elix_renal_sev),
elix_hypo = max(.data$elix_hypo),
elix_thyroid_oth = max(.data$elix_thyroid_oth),
elix_peptic = max(.data$elix_peptic),
elix_valve = max(.data$elix_valve),
elix_weightloss = max(.data$elix_weightloss)) %>%
dplyr::ungroup()
message("Message: Currently there are no weights available for ICD-10.")
}
dat4 <- dat3 %>%
dplyr::select(id, tidyselect::starts_with("elix"))
if (version == 9 | version == 19){
dat4 <- dat4 %>%
dplyr::rename(chf = .data$elix_chf,
valve = .data$elix_valve,
pulmcirc = .data$elix_pulmcirc,
perivasc = .data$elix_periph_vasc,
htn_c = .data$elix_htn_comb,
para = .data$elix_paralysis,
neuro = .data$elix_neuro,
chrnlung = .data$elix_chronic_pulm,
dm = .data$elix_diab_uc,
dmcx = .data$elix_diab_c,
hypothy = .data$elix_hypo,
renlfail = .data$elix_renal,
liver = .data$elix_liver,
ulcer = .data$elix_peptic,
aids = .data$elix_hiv,
lymph = .data$elix_lymph,
mets = .data$elix_mets,
tumor = .data$elix_tumor,
arth = .data$elix_rheum,
coag = .data$elix_coag,
obese = .data$elix_obese,
wghtloss = .data$elix_weightloss,
lytes = .data$elix_fluid,
bldloss = .data$elix_bld_anem,
anemdef = .data$elix_def_anem,
alcohol = .data$elix_alcohol,
drug = .data$elix_drug,
psych = .data$elix_psych,
depress = .data$elix_depression)
}
else{
dat4 <- dat4 %>%
dplyr::rename(aids = .data$elix_aids,
alcohol = .data$elix_alcohol,
anemdef = .data$elix_def_anem,
arth = .data$elix_rheum,
bldloss = .data$elix_bld_loss,
cancer_leuk = .data$elix_cancer_leuk,
cancer_lymph = .data$elix_cancer_lymph,
cancer_mets = .data$elix_cancer_mets,
cancer_nsitu = .data$elix_cancer_insitu,
cancer_solid = .data$elix_cancer_solid,
cbvd = .data$elix_cbvd,
chf = .data$elix_chf,
coag = .data$elix_coag,
dementia = .data$elix_dementia,
depress = .data$elix_depress,
diab_cx = .data$elix_diab_c,
diab_uncx = .data$elix_diab_uc,
drug_abuse = .data$elix_drug,
htn_cx = .data$elix_htn_c,
htn_uncx = .data$elix_htn_uc,
liver_mld = .data$elix_liver_mild,
liver_sev = .data$elix_liver_sev,
lung_chronic = .data$elix_chronic_pulm,
neuro_movt = .data$elix_neuro_movt,
neuro_oth = .data$elix_neuro_seiz,
neuro_seiz = .data$elix_neuro_oth,
obese = .data$elix_obese,
paralysis = .data$elix_paralysis,
perivasc = .data$elix_perivasc,
psychoses = .data$elix_psych,
pulmcirc = .data$elix_pulmcirc,
renlfl_mod = .data$elix_renal_mod,
renlfl_sev = .data$elix_renal_sev,
thyroid_hypo = .data$elix_hypo,
thyroid_oth = .data$elix_thyroid_oth,
ulcer_peptic = .data$elix_peptic,
valve = .data$elix_valve,
wghtloss = .data$elix_weightloss)
}
return(dat4)
}
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