R/hsmr_hid.R
In Public-Health-Scotland/hsmr: Reproducible Analytical Pipeline of Hospital Standardised Mortality Ratios Quarterly Publication
Defines functions
hsmr_hid
Documented in
hsmr_hid
#' @title Hospital Intelligence Dashboard.
#'
#' @description \code{hsmr_hid} reformats the output from \code{smr_data}
#' and \code{trend_data} in order to fit the template agreed for HID.
#' It adds variables \code{scot_ratio}, \code{Topic}, \code{Indicator}
#' and \code{Frequency}; and reformats \code{location}, \code{hb}.
#' Dropping all other variables except the following which are renamed:
#' \code{hb}, \code{location_name}, \code{deaths}, \code{pred}, \code{pats},
#' \code{smr}, \code{crd_rate}, \code{death_scot}, \code{scot_deaths},
#' \code{pred_scot}, \code{scot_pats} and \code{st_err}.
#'
#' @details \href{https://www.isdscotland.org/Health-Topics/Quality-Indicators/
#' Hospital-Scorecard//}{Hospital Intelligence Dashboard} is a management
#' information system to be interpreted and used nationally by the Scottish
#' Government and locally by NHS Boards and clinicians. It allows comparison
#' of each NHS Boards' performance against the national average, and provides
#' trend analysis to help monitor variation over time for each indicator where
#' appropriate. The data are presented by NHS Board and hospital of treatment.
#'
#' @param data The input \code{tibble} which is the output from \code{smr_data}
#' or \code{create_trends}.
#'
#' @return If the class is not initiated correctly, nothing is returned.
#'
#' @importFrom magrittr %>%
#' @importFrom magrittr %<>%
#'
#' @export
hsmr_hid <- function(smr_data, trend_data, end_date){
### 1 - Error handling ----
if (class(end_date) != "Date") {
stop("The extract end date must be provided in date format")
}
if(!(format(end_date, "%d %B") %in% c("31 March",
"30 June",
"30 September",
"31 December"))) {
stop("The extract end date must be the final day of either March, June, ",
"September or December")
}
### 2 - Reformat SMR Data ----
if(!all(c("deaths", "pred", "pats", "smr", "crd_rate",
"location", "hb", "location_name",
"period_label", "death_scot", "pred_scot",
"pats_scot", "smr_scot") %in% names(smr_data))) {
stop(paste0("For HID data for HSMR, input_data object must be ",
"output from smr_data()"))}
hsmr_data<-smr_data %<>%
tidylog::filter(period == 3 & location %in%
c("C206H", "C418H", "Y104H", "Y146H", "N101H", "A101H", "R101H",
"H212H", "B120H", "H103H", "N411H", "Y146H", "V217H", "Y144H",
"Z102H", "G107H", "D102H", "C313H", "C121H", "G306H", "T101H",
"T202H", "G405H", "F805H", "H202H", "C418H", "S314H", "S308H",
"G207H", "T312H", "A210H", "A111H", "L302H", "L106H", "L308H",
"F704H", "S116H", "W107H", "G516H",
"S08000015", "S08000016", "S08000017", "S08000029",
"S08000019", "S08000020", "S08000031", "S08000022",
"S08000032", "S08000024", "S08000025", "S08000026",
"S08000030", "S08000028", "S08100001",
"Scot")) %>%
tidylog::mutate(
hosp_code = dplyr::case_when(
location == "S08000015" ~ "A",
location == "S08000016" ~ "B",
location == "S08000017" ~ "Y",
location == "S08000029" ~ "F",
location == "S08000019" ~ "V",
location == "S08000020" ~ "N",
location == "S08000031" ~ "G",
location == "S08000022" ~ "H",
location == "S08000032" ~ "L",
location == "S08000024" ~ "S",
location == "S08000025" ~ "R",
location == "S08000026" ~ "Z",
location == "S08000030" ~ "T",
location == "S08000028" ~ "W",
location == "S08100001" ~ "D",
TRUE ~ as.character(location)),
HBName = dplyr::case_when(
hb == "S08000015" ~ "Ayrshire & Arran",
hb == "S08000016" ~ "Borders",
hb == "S08000017" ~ "Dumfries & Galloway",
hb == "S08000029" ~ "Fife",
hb == "S08000019" ~ "Forth Valley",
hb == "S08000020" ~ "Grampian",
hb == "S08000031" ~ "Greater Glasgow & Clyde",
hb == "S08000022" ~ "Highland",
hb == "S08000032" ~ "Lanarkshire",
hb == "S08000024" ~ "Lothian",
hb == "S08000025" ~ "Orkney",
hb == "S08000026" ~ "Shetland",
hb == "S08000030" ~ "Tayside",
hb == "S08000028" ~ "Western Isles",
hb == "S08100001" ~ "Golden Jubilee",
hb == "Scotland" ~ "Scotland"),
HealthBoard = dplyr::case_when(
hb == "S08000015" ~ "NHS Ayrshire & Arran",
hb == "S08000016" ~ "NHS Borders",
hb == "S08000017" ~ "NHS Dumfries & Galloway",
hb == "S08000029" ~ "NHS Fife",
hb == "S08000019" ~ "NHS Forth Valley",
hb == "S08000020" ~ "NHS Grampian",
hb == "S08000031" ~ "NHS Greater Glasgow & Clyde",
hb == "S08000022" ~ "NHS Highland",
hb == "S08000032" ~ "NHS Lanarkshire",
hb == "S08000024" ~ "NHS Lothian",
hb == "S08000025" ~ "NHS Orkney",
hb == "S08000026" ~ "NHS Shetland",
hb == "S08000030" ~ "NHS Tayside",
hb == "S08000028" ~ "NHS Western Isles",
hb == "S08100001" ~ "Golden Jubilee",
hb == "Scotland" ~ "Scotland"),
scot_ratio = 1,
stdev = as.character(round(st_err, digits=8)),
Topic = "HSMR",
Indicator = "HSMR",
# Dealing with cases when month is one or two digits
date_label = case_when(nchar(lubridate::month(end_date) - 2) == 1 ~
paste("01", paste0("0", lubridate::month(end_date) - 2),
lubridate::year(end_date), sep = "/"),
T ~ paste("01", lubridate::month(end_date) - 2,
lubridate::year(end_date), sep = "/")),
Frequency = "Quarterly") %>%
tidylog::select(hosp_code, hb, location_name, HBName, HealthBoard,
deaths, pred, smr, death_scot, pred_scot,
scot_ratio, stdev, Topic, Indicator, date_label, Frequency)%>%
dplyr::rename(hb_code=hb, Location=location_name, numerator=deaths,
denominator=pred,ratio=smr,scot_num=death_scot,
scot_denom=pred_scot)
### 3 - Reformat Crude data ----
if(!all(c("hb", "location", "location_name", "agg_label", "quarter",
"quarter_short", "quarter_full", "sub_grp", "label",
"scot_deaths", "scot_pats", "deaths", "pats",
"crd_rate") %in% names(trend_data))) {
stop(paste0("For NHS Performs data for Crude Rates, input_data object ",
"must be output from create_trends()"))}
crude_data<-trend_data %<>%
tidylog::filter(sub_grp == "All admissions") %>%
tidylog::mutate(
hosp_code = dplyr::case_when(
location == "S08000015" ~ "A",
location == "S08000016" ~ "B",
location == "S08000017" ~ "Y",
location == "S08000029" ~ "F",
location == "S08000019" ~ "V",
location == "S08000020" ~ "N",
location == "S08000031" ~ "G",
location == "S08000022" ~ "H",
location == "S08000032" ~ "L",
location == "S08000024" ~ "S",
location == "S08000025" ~ "R",
location == "S08000026" ~ "Z",
location == "S08000030" ~ "T",
location == "S08000028" ~ "W",
location == "S08100001" ~ "D",
TRUE ~ as.character(location)),
HBName = dplyr::case_when(
hb == "S08000015" ~ "Ayrshire & Arran",
hb == "S08000016" ~ "Borders",
hb == "S08000017" ~ "Dumfries & Galloway",
hb == "S08000029" ~ "Fife",
hb == "S08000019" ~ "Forth Valley",
hb == "S08000020" ~ "Grampian",
hb == "S08000031" ~ "Greater Glasgow & Clyde",
hb == "S08000022" ~ "Highland",
hb == "S08000032" ~ "Lanarkshire",
hb == "S08000024" ~ "Lothian",
hb == "S08000025" ~ "Orkney",
hb == "S08000026" ~ "Shetland",
hb == "S08000030" ~ "Tayside",
hb == "S08000028" ~ "Western Isles",
hb == "S08100001" ~ "Golden Jubilee",
hb == "Scotland" ~ "Scotland"),
HealthBoard = dplyr::case_when(
hb == "S08000015" ~ "NHS Ayrshire & Arran",
hb == "S08000016" ~ "NHS Borders",
hb == "S08000017" ~ "NHS Dumfries & Galloway",
hb == "S08000029" ~ "NHS Fife",
hb == "S08000019" ~ "NHS Forth Valley",
hb == "S08000020" ~ "NHS Grampian",
hb == "S08000031" ~ "NHS Greater Glasgow & Clyde",
hb == "S08000022" ~ "NHS Highland",
hb == "S08000032" ~ "NHS Lanarkshire",
hb == "S08000024" ~ "NHS Lothian",
hb == "S08000025" ~ "NHS Orkney",
hb == "S08000026" ~ "NHS Shetland",
hb == "S08000030" ~ "NHS Tayside",
hb == "S08000028" ~ "NHS Western Isles",
hb == "S08100001" ~ "Golden Jubilee",
hb == "Scotland" ~ "Scotland"),
scot_ratio = (scot_deaths/scot_pats)*100,
stdev = " ",
Topic = "HSMR",
Indicator = "Crude Mortality rates within 30-days",
date_label = dplyr::case_when(substr(quarter_short, 1, 3) == "Apr" ~
paste0("01/04/", substr(quarter_short,
9, 12)),
substr(quarter_short, 1, 3) == "Jul" ~
paste0("01/07/", substr(quarter_short,
9, 12)),
substr(quarter_short, 1, 3) == "Oct" ~
paste0("01/10/", substr(quarter_short,
9, 12)),
substr(quarter_short, 1, 3) == "Jan" ~
paste0("01/01/", substr(quarter_short,
9, 12))),
Frequency = "Quarterly") %>%
tidylog::select(hosp_code, hb, location_name, HBName, HealthBoard,
deaths, pats, crd_rate, scot_deaths, scot_pats,
scot_ratio, stdev, Topic, Indicator, date_label, Frequency)%>%
dplyr::rename(hb_code=hb, Location=location_name, numerator=deaths,
denominator=pats,ratio=crd_rate,scot_num=scot_deaths,
scot_denom=scot_pats)
#4 - Combine smr and crude data into one file
hid_data<-dplyr::bind_rows(hsmr_data, crude_data)
return(hid_data)
}
Public-Health-Scotland/hsmr documentation built on June 24, 2024, 1:48 a.m.
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Defines functions hsmr_hid
Documented in hsmr_hid
#' @title Hospital Intelligence Dashboard.
#'
#' @description \code{hsmr_hid} reformats the output from \code{smr_data}
#' and \code{trend_data} in order to fit the template agreed for HID.
#' It adds variables \code{scot_ratio}, \code{Topic}, \code{Indicator}
#' and \code{Frequency}; and reformats \code{location}, \code{hb}.
#' Dropping all other variables except the following which are renamed:
#' \code{hb}, \code{location_name}, \code{deaths}, \code{pred}, \code{pats},
#' \code{smr}, \code{crd_rate}, \code{death_scot}, \code{scot_deaths},
#' \code{pred_scot}, \code{scot_pats} and \code{st_err}.
#'
#' @details \href{https://www.isdscotland.org/Health-Topics/Quality-Indicators/
#' Hospital-Scorecard//}{Hospital Intelligence Dashboard} is a management
#' information system to be interpreted and used nationally by the Scottish
#' Government and locally by NHS Boards and clinicians. It allows comparison
#' of each NHS Boards' performance against the national average, and provides
#' trend analysis to help monitor variation over time for each indicator where
#' appropriate. The data are presented by NHS Board and hospital of treatment.
#'
#' @param data The input \code{tibble} which is the output from \code{smr_data}
#' or \code{create_trends}.
#'
#' @return If the class is not initiated correctly, nothing is returned.
#'
#' @importFrom magrittr %>%
#' @importFrom magrittr %<>%
#'
#' @export
hsmr_hid <- function(smr_data, trend_data, end_date){
### 1 - Error handling ----
if (class(end_date) != "Date") {
stop("The extract end date must be provided in date format")
}
if(!(format(end_date, "%d %B") %in% c("31 March",
"30 June",
"30 September",
"31 December"))) {
stop("The extract end date must be the final day of either March, June, ",
"September or December")
}
### 2 - Reformat SMR Data ----
if(!all(c("deaths", "pred", "pats", "smr", "crd_rate",
"location", "hb", "location_name",
"period_label", "death_scot", "pred_scot",
"pats_scot", "smr_scot") %in% names(smr_data))) {
stop(paste0("For HID data for HSMR, input_data object must be ",
"output from smr_data()"))}
hsmr_data<-smr_data %<>%
tidylog::filter(period == 3 & location %in%
c("C206H", "C418H", "Y104H", "Y146H", "N101H", "A101H", "R101H",
"H212H", "B120H", "H103H", "N411H", "Y146H", "V217H", "Y144H",
"Z102H", "G107H", "D102H", "C313H", "C121H", "G306H", "T101H",
"T202H", "G405H", "F805H", "H202H", "C418H", "S314H", "S308H",
"G207H", "T312H", "A210H", "A111H", "L302H", "L106H", "L308H",
"F704H", "S116H", "W107H", "G516H",
"S08000015", "S08000016", "S08000017", "S08000029",
"S08000019", "S08000020", "S08000031", "S08000022",
"S08000032", "S08000024", "S08000025", "S08000026",
"S08000030", "S08000028", "S08100001",
"Scot")) %>%
tidylog::mutate(
hosp_code = dplyr::case_when(
location == "S08000015" ~ "A",
location == "S08000016" ~ "B",
location == "S08000017" ~ "Y",
location == "S08000029" ~ "F",
location == "S08000019" ~ "V",
location == "S08000020" ~ "N",
location == "S08000031" ~ "G",
location == "S08000022" ~ "H",
location == "S08000032" ~ "L",
location == "S08000024" ~ "S",
location == "S08000025" ~ "R",
location == "S08000026" ~ "Z",
location == "S08000030" ~ "T",
location == "S08000028" ~ "W",
location == "S08100001" ~ "D",
TRUE ~ as.character(location)),
HBName = dplyr::case_when(
hb == "S08000015" ~ "Ayrshire & Arran",
hb == "S08000016" ~ "Borders",
hb == "S08000017" ~ "Dumfries & Galloway",
hb == "S08000029" ~ "Fife",
hb == "S08000019" ~ "Forth Valley",
hb == "S08000020" ~ "Grampian",
hb == "S08000031" ~ "Greater Glasgow & Clyde",
hb == "S08000022" ~ "Highland",
hb == "S08000032" ~ "Lanarkshire",
hb == "S08000024" ~ "Lothian",
hb == "S08000025" ~ "Orkney",
hb == "S08000026" ~ "Shetland",
hb == "S08000030" ~ "Tayside",
hb == "S08000028" ~ "Western Isles",
hb == "S08100001" ~ "Golden Jubilee",
hb == "Scotland" ~ "Scotland"),
HealthBoard = dplyr::case_when(
hb == "S08000015" ~ "NHS Ayrshire & Arran",
hb == "S08000016" ~ "NHS Borders",
hb == "S08000017" ~ "NHS Dumfries & Galloway",
hb == "S08000029" ~ "NHS Fife",
hb == "S08000019" ~ "NHS Forth Valley",
hb == "S08000020" ~ "NHS Grampian",
hb == "S08000031" ~ "NHS Greater Glasgow & Clyde",
hb == "S08000022" ~ "NHS Highland",
hb == "S08000032" ~ "NHS Lanarkshire",
hb == "S08000024" ~ "NHS Lothian",
hb == "S08000025" ~ "NHS Orkney",
hb == "S08000026" ~ "NHS Shetland",
hb == "S08000030" ~ "NHS Tayside",
hb == "S08000028" ~ "NHS Western Isles",
hb == "S08100001" ~ "Golden Jubilee",
hb == "Scotland" ~ "Scotland"),
scot_ratio = 1,
stdev = as.character(round(st_err, digits=8)),
Topic = "HSMR",
Indicator = "HSMR",
# Dealing with cases when month is one or two digits
date_label = case_when(nchar(lubridate::month(end_date) - 2) == 1 ~
paste("01", paste0("0", lubridate::month(end_date) - 2),
lubridate::year(end_date), sep = "/"),
T ~ paste("01", lubridate::month(end_date) - 2,
lubridate::year(end_date), sep = "/")),
Frequency = "Quarterly") %>%
tidylog::select(hosp_code, hb, location_name, HBName, HealthBoard,
deaths, pred, smr, death_scot, pred_scot,
scot_ratio, stdev, Topic, Indicator, date_label, Frequency)%>%
dplyr::rename(hb_code=hb, Location=location_name, numerator=deaths,
denominator=pred,ratio=smr,scot_num=death_scot,
scot_denom=pred_scot)
### 3 - Reformat Crude data ----
if(!all(c("hb", "location", "location_name", "agg_label", "quarter",
"quarter_short", "quarter_full", "sub_grp", "label",
"scot_deaths", "scot_pats", "deaths", "pats",
"crd_rate") %in% names(trend_data))) {
stop(paste0("For NHS Performs data for Crude Rates, input_data object ",
"must be output from create_trends()"))}
crude_data<-trend_data %<>%
tidylog::filter(sub_grp == "All admissions") %>%
tidylog::mutate(
hosp_code = dplyr::case_when(
location == "S08000015" ~ "A",
location == "S08000016" ~ "B",
location == "S08000017" ~ "Y",
location == "S08000029" ~ "F",
location == "S08000019" ~ "V",
location == "S08000020" ~ "N",
location == "S08000031" ~ "G",
location == "S08000022" ~ "H",
location == "S08000032" ~ "L",
location == "S08000024" ~ "S",
location == "S08000025" ~ "R",
location == "S08000026" ~ "Z",
location == "S08000030" ~ "T",
location == "S08000028" ~ "W",
location == "S08100001" ~ "D",
TRUE ~ as.character(location)),
HBName = dplyr::case_when(
hb == "S08000015" ~ "Ayrshire & Arran",
hb == "S08000016" ~ "Borders",
hb == "S08000017" ~ "Dumfries & Galloway",
hb == "S08000029" ~ "Fife",
hb == "S08000019" ~ "Forth Valley",
hb == "S08000020" ~ "Grampian",
hb == "S08000031" ~ "Greater Glasgow & Clyde",
hb == "S08000022" ~ "Highland",
hb == "S08000032" ~ "Lanarkshire",
hb == "S08000024" ~ "Lothian",
hb == "S08000025" ~ "Orkney",
hb == "S08000026" ~ "Shetland",
hb == "S08000030" ~ "Tayside",
hb == "S08000028" ~ "Western Isles",
hb == "S08100001" ~ "Golden Jubilee",
hb == "Scotland" ~ "Scotland"),
HealthBoard = dplyr::case_when(
hb == "S08000015" ~ "NHS Ayrshire & Arran",
hb == "S08000016" ~ "NHS Borders",
hb == "S08000017" ~ "NHS Dumfries & Galloway",
hb == "S08000029" ~ "NHS Fife",
hb == "S08000019" ~ "NHS Forth Valley",
hb == "S08000020" ~ "NHS Grampian",
hb == "S08000031" ~ "NHS Greater Glasgow & Clyde",
hb == "S08000022" ~ "NHS Highland",
hb == "S08000032" ~ "NHS Lanarkshire",
hb == "S08000024" ~ "NHS Lothian",
hb == "S08000025" ~ "NHS Orkney",
hb == "S08000026" ~ "NHS Shetland",
hb == "S08000030" ~ "NHS Tayside",
hb == "S08000028" ~ "NHS Western Isles",
hb == "S08100001" ~ "Golden Jubilee",
hb == "Scotland" ~ "Scotland"),
scot_ratio = (scot_deaths/scot_pats)*100,
stdev = " ",
Topic = "HSMR",
Indicator = "Crude Mortality rates within 30-days",
date_label = dplyr::case_when(substr(quarter_short, 1, 3) == "Apr" ~
paste0("01/04/", substr(quarter_short,
9, 12)),
substr(quarter_short, 1, 3) == "Jul" ~
paste0("01/07/", substr(quarter_short,
9, 12)),
substr(quarter_short, 1, 3) == "Oct" ~
paste0("01/10/", substr(quarter_short,
9, 12)),
substr(quarter_short, 1, 3) == "Jan" ~
paste0("01/01/", substr(quarter_short,
9, 12))),
Frequency = "Quarterly") %>%
tidylog::select(hosp_code, hb, location_name, HBName, HealthBoard,
deaths, pats, crd_rate, scot_deaths, scot_pats,
scot_ratio, stdev, Topic, Indicator, date_label, Frequency)%>%
dplyr::rename(hb_code=hb, Location=location_name, numerator=deaths,
denominator=pats,ratio=crd_rate,scot_num=scot_deaths,
scot_denom=scot_pats)
#4 - Combine smr and crude data into one file
hid_data<-dplyr::bind_rows(hsmr_data, crude_data)
return(hid_data)
}
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