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| export(comorbidity) | ||
| export(sample_diag) | ||
| export(score) | ||
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| #' @keywords internal | ||
| .check_output <- function(x, id, score) { | ||
| .check_output <- function(x, id) { | ||
| x[[id]] <- NULL | ||
| if (score == "charlson") { | ||
| x[["score"]] <- NULL | ||
| x[["index"]] <- NULL | ||
| x[["wscore"]] <- NULL | ||
| x[["windex"]] <- NULL | ||
| } else if (score == "elixhauser") { | ||
| x[["score"]] <- NULL | ||
| x[["index"]] <- NULL | ||
| x[["wscore_ahrq"]] <- NULL | ||
| x[["wscore_vw"]] <- NULL | ||
| x[["windex_ahrq"]] <- NULL | ||
| x[["windex_vw"]] <- NULL | ||
| } | ||
| # Check that all identified comorbidites are either 0 or 1 | ||
| # Check that all identified comorbidity domains are either 0 or 1 | ||
| if (!all(x == 0 | x == 1)) stop("'comorbidity' ended up in an unexpected state.\nPlease report a bug with a reproducible example at https://github.com/ellessenne/comorbidity/issues\n", call. = FALSE) | ||
| } |
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| #' @keywords internal | ||
| .codes_to_regex <- function(x) { | ||
| x <- paste(x, collapse = "|^") | ||
| x <- paste0("^", x) | ||
| return(x) | ||
| } |
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| # ### Compute Charlson score and Charlson index | ||
| # if (score == "charlson") { | ||
| # x$score <- with(x, ami + chf + pvd + cevd + dementia + copd + rheumd + pud + mld * ifelse(msld == 1 & assign0 != "none", 0, 1) + diab * ifelse(diabwc == 1 & assign0 != "none", 0, 1) + diabwc + hp + rend + canc * ifelse(metacanc == 1 & assign0 != "none", 0, 1) + msld + metacanc + aids) | ||
| # x$index <- with(x, cut(score, breaks = c(0, 1, 2.5, 4.5, Inf), labels = c("0", "1-2", "3-4", ">=5"), right = FALSE)) | ||
| # x$wscore <- with(x, ami + chf + pvd + cevd + dementia + copd + rheumd + pud + mld * ifelse(msld == 1 & assign0 != "none", 0, 1) + diab * ifelse(diabwc == 1 & assign0 != "none", 0, 1) + diabwc * 2 + hp * 2 + rend * 2 + canc * ifelse(metacanc == 1 & assign0 != "none", 0, 2) + msld * 3 + metacanc * 6 + aids * 6) | ||
| # x$windex <- with(x, cut(wscore, breaks = c(0, 1, 2.5, 4.5, Inf), labels = c("0", "1-2", "3-4", ">=5"), right = FALSE)) | ||
| # } else { | ||
| # x$score <- with(x, chf + carit + valv + pcd + pvd + hypunc * ifelse(hypc == 1 & assign0 != "none", 0, 1) + hypc + para + ond + cpd + diabunc * ifelse(diabc == 1 & assign0 != "none", 0, 1) + diabc + hypothy + rf + ld + pud + aids + lymph + metacanc + solidtum * ifelse(metacanc == 1 & assign0 != "none", 0, 1) + rheumd + coag + obes + wloss + fed + blane + dane + alcohol + drug + psycho + depre) | ||
| # x$index <- with(x, cut(score, breaks = c(-Inf, 0, 1, 4.5, Inf), labels = c("<0", "0", "1-4", ">=5"), right = FALSE)) | ||
| # x$wscore_ahrq <- with(x, chf * 9 + carit * 0 + valv * 0 + pcd * 6 + pvd * 3 + ifelse(hypunc == 1 | hypc == 1, 1, 0) * (-1) + para * 5 + ond * 5 + cpd * 3 + diabunc * ifelse(diabc == 1 & assign0 != "none", 0, 0) + diabc * (-3) + hypothy * 0 + rf * 6 + ld * 4 + pud * 0 + aids * 0 + lymph * 6 + metacanc * 14 + solidtum * ifelse(metacanc == 1 & assign0 != "none", 0, 7) + rheumd * 0 + coag * 11 + obes * (-5) + wloss * 9 + fed * 11 + blane * (-3) + dane * (-2) + alcohol * (-1) + drug * (-7) + psycho * (-5) + depre * (-5)) | ||
| # x$wscore_vw <- with(x, chf * 7 + carit * 5 + valv * (-1) + pcd * 4 + pvd * 2 + ifelse(hypunc == 1 | hypc == 1, 1, 0) * 0 + para * 7 + ond * 6 + cpd * 3 + diabunc * ifelse(diabc == 1 & assign0 != "none", 0, 0) + diabc * 0 + hypothy * 0 + rf * 5 + ld * 11 + pud * 0 + aids * 0 + lymph * 9 + metacanc * 12 + solidtum * ifelse(metacanc == 1 & assign0 != "none", 0, 4) + rheumd * 0 + coag * 3 + obes * (-4) + wloss * 6 + fed * 5 + blane * (-2) + dane * (-2) + alcohol * 0 + drug * (-7) + psycho * 0 + depre * (-3)) | ||
| # x$windex_ahrq <- with(x, cut(wscore_ahrq, breaks = c(-Inf, 0, 1, 4.5, Inf), labels = c("<0", "0", "1-4", ">=5"), right = FALSE)) | ||
| # x$windex_vw <- with(x, cut(wscore_vw, breaks = c(-Inf, 0, 1, 4.5, Inf), labels = c("<0", "0", "1-4", ">=5"), right = FALSE)) | ||
| # } | ||
| # | ||
| # ### If 'assign0 = "both"', then apply hierarchy to individual comorbidity domains too | ||
| # if (assign0 == "both") { | ||
| # if (score == "charlson") { | ||
| # # "Mild liver disease" (`mld`) and "Moderate/severe liver disease" (`msld`) | ||
| # x$mld[x$msld == 1] <- 0 | ||
| # # "Diabetes" (`diab`) and "Diabetes with complications" (`diabwc`) | ||
| # x$diab[x$diabwc == 1] <- 0 | ||
| # # "Cancer" (`canc`) and "Metastatic solid tumour" (`metacanc`) | ||
| # x$canc[x$metacanc == 1] <- 0 | ||
| # } else { | ||
| # # "Hypertension, uncomplicated" (`hypunc`) and "Hypertension, complicated" (`hypc`) | ||
| # x$hypunc[x$hypc == 1] <- 0 | ||
| # # "Diabetes, uncomplicated" (`diabunc`) and "Diabetes, complicated" (`diabc`) | ||
| # x$diabunc[x$diabc == 1] <- 0 | ||
| # # "Solid tumour" (`solidtum`) and "Metastatic cancer" (`metacanc`) | ||
| # x$solidtum[x$metacanc == 1] <- 0 | ||
| # } | ||
| # } | ||
| # } | ||
| #' @export | ||
| score <- function(x, weights = NULL, assign0) { | ||
| ### First, check the function is getting a 'comorbidity' data.frame | ||
| if (!inherits(x = x, what = "comorbidity")) { | ||
| stop("This function can only be used on an object of class 'comorbidity', which you can obtain by using the 'comorbidity()' function. See ?comorbidity for more details.", call. = FALSE) | ||
| } | ||
| ### Check arguments | ||
| arg_checks <- checkmate::makeAssertCollection() | ||
| # weights must be a single string value | ||
| checkmate::assert_string(weights, add = arg_checks) | ||
| # weights must be one of the supported; case insensitive | ||
| weights <- tolower(weights) | ||
| checkmate::assert_choice(weights, choices = c("vw", "ahrq"), add = arg_checks) | ||
| # assign0 be a single boolean value | ||
| checkmate::assert_logical(assign0, add = arg_checks) | ||
| # Report if there are any errors | ||
| if (!arg_checks$isEmpty()) checkmate::reportAssertions(arg_checks) | ||
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| map <- attr(x = x, which = "map") | ||
| print(map) | ||
| } |
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