get_spec_rt: Calculate specific rates

In bcgov/bcEpiRate: Tools for Standardized Rates in Population Health Surveillance and Epidemiology

Description

Calculate specific rates given a vector containing the frequencies of events and a vector containing the sizes of the defined populations.

Usage

get_spec_rt(
  counts,
  popn,
  scale = NULL,
  power = NULL,
  output_status = FALSE,
  dist = NULL,
  interval = NULL
)

Arguments

counts	A numeric vector containing the frequency of events.
popn	A numeric vector containing the size of each defined population.
scale, power	Provide either scale, a positive integer, to specify the scale, or power, a non-negative integer, to specify the power of 10 to use when expressing the result. If neither are supplied, scale = 1 will be applied.
output_status	If FALSE (default) the calculated rates are returned as a numeric vector. If TRUE a data frame containing both the rates and the validity of the corresponding elements in the input vectors is returned.
dist	A string to indicate the type of probability distribution for the confidence interval to follow. Can be one of the following: "normal", "log normal" or "poisson". This parameter is case insensitive.
interval	A scalar, between 0 and 1, indicating the width of the confidence interval. For example, for a 95% confidence interval, use interval = 0.95.

Details

This low-level function assumes that counts and sizes of respective subpopulations are provided in the same order. It can also be used to calculate a crude rate if counts and popn are scalars and represent the sum of all counts and the size of the entire population respectively.

To construct confidence intervals for the rate estimates, arguments must be explicitly supplied to both dist and interval.

Value

If output_status = FALSE and neither dist or interval is supplied, a numeric vector is returned.

Otherwise, a data frame is returned with a column for rate and up to 4 additional columns:

• If output_status = TRUE, then the column status is included.

• If both dist and interval are provided, then the columns interval, lower, and upper are also included.

The status column of the output can be interpreted as follows:

• "has_NA" indicates that the numerator and/or denominator of the fraction was NA.

• "denom_0" indicates that the denominator of the fraction was 0.

• "success" indicates that both the numerator and denominator of the fraction were valid numbers.

References

The STDRATE Procedure

See Also

get_ci_norm(), get_ci_lnorm(), get_ci_pois()

Examples

## Not run: 
# using vectors
counts <- c(100, 200, 300, 400, 500)
popn <- c(1000, 5000, 10000, 50000, 100000)

get_spec_rt(counts, popn)
get_spec_rt(counts, popn, scale = 1000)
get_spec_rt(counts, popn, power = 3)

# get output status
get_spec_rt(counts, popn, output_status = TRUE)

# construct confidence intervals for rate estimates
get_spec_rt(counts, popn, dist = "normal", interval = 0.95)

# using a data frame
df <- data.frame(counts, popn)

get_spec_rt(df$counts, df$popn, scale = 100000)
get_spec_rt(df$counts, df$popn, power = 5)

# using dplyr to create a column
df <- df %>%
  dplyr::mutate(spec_rate = get_spec_rt(counts, popn, scale = 1000))

## End(Not run)

bcgov/bcEpiRate documentation built on Feb. 24, 2022, 4:05 p.m.