PHEindicatormethods (version 1.4.2)

phe_smr: Calculate Indirectly Standardised Ratio (Standardised Mortality Ratio or Standardised Admission Ratio) using calculate_ISRatio

Description

To prevent ambiguity over the ISR acronym, the phe_smr function has been replaced with a calculate_ISRatio function. Both functions take the same parameters and provide identical functionality. The phe_smr function will remain available in the PHEindicatormethods package until at least December 2022 to allow users time to transfer existing code to use the new calculate_ISRatio function. Please refer to the calculate_ISRatio documentation for full support on the use of these functions.

Usage

phe_smr(
  data,
  x,
  n,
  x_ref,
  n_ref,
  refpoptype = "vector",
  type = "full",
  confidence = 0.95,
  refvalue = 1
)

Arguments

data

data.frame containing the data to be standardised, pre-grouped if multiple ISRs required; unquoted string; no default

x

field name from data containing the observed number of events for each standardisation category (eg ageband) within each grouping set (eg area); unquoted string; no default

n

field name from data containing the populations for each standardisation category (eg ageband) within each grouping set (eg area); unquoted string; no default

x_ref

the observed number of events in the reference population for each standardisation category (eg age band); unquoted numeric vector or field name from data depending on value of refpoptype; no default

n_ref

the reference population for each standardisation category (eg age band); unquoted numeric vector or field name from data depending on value of refpoptype; no default

refpoptype

whether x_ref and n_ref have been specified as vectors or a field name from data; quoted string "field" or "vector"; default = "vector"

type

defines the data and metadata columns to be included in output; can be "value", "lower", "upper", "standard" (for all data) or "full" (for all data and metadata); quoted string; default = "full"

confidence

the required level of confidence expressed as a number between 0.9 and 1 or a number between 90 and 100 or can be a vector of 0.95 and 0.998, for example, to output both 95 percent and 99.8 percent percent CIs; numeric; default 0.95

refvalue

the standardised reference ratio, numeric, default = 1

Examples

library(dplyr)
df <- data.frame(indicatorid = rep(c(1234, 5678, 91011, 121314), each = 19 * 2 * 5),
                 year = rep(2006:2010, each = 19 * 2),
                 sex = rep(rep(c("Male", "Female"), each = 19), 5),
                 ageband = rep(c(0,5,10,15,20,25,30,35,40,45,
                                 50,55,60,65,70,75,80,85,90), times = 10),
                 obs = sample(200, 19 * 2 * 5 * 4, replace = TRUE),
                 pop = sample(10000:20000, 19 * 2 * 5 * 4, replace = TRUE))

refdf <- data.frame(refcount = sample(200, 19, replace = TRUE),
                    refpop = sample(10000:20000, 19, replace = TRUE))

df %>%
    group_by(indicatorid, year, sex) %>%
    phe_smr(obs, pop, refdf$refcount, refdf$refpop, type="standard")

## OR

df %>%
    group_by(indicatorid, year, sex) %>%
    phe_smr(obs, pop, refdf$refcount, refdf$refpop, confidence=99.8, refvalue=100)