An ensemble operation (`ens_` family). It dispatches on the ensemble class, so the class – not a name prefix on the caller – carries the "operates on an ensemble" meaning. That matches [nowcast_quasipoisson_v1()] and [short_term_trend()].
Usage
ens_add_rate(x, ...)
# S3 method for class 'csfmt_ensemble_v3'
ens_add_rate(x, numerator, denominator, per = 100, name = NULL, ...)See also
vignette("pipeline", package = "csalert"), which runs this
function as stage 4 of its pipeline, on a numerator and denominator that
were nowcast together.
Other ensemble operations:
ens_collapse()
Examples
d <- data.table::data.table(
location_code = "nation",
age = "total",
isoyearweek = c("2023-01", "2023-02", "2023-03")
)
# The numerator must be a SUBSET of the denominator (tests positive out of
# tests taken), so simulate the denominator first and the numerator
# conditionally on it. Two independent Poissons would not be a proportion.
set.seed(1)
denom <- matrix(rpois(3 * 100, 200), nrow = 3)
numer <- matrix(rbinom(length(denom), size = denom, prob = 0.10), nrow = 3)
ens <- csfmt_ensemble_v3(
d,
id_cols = c("location_code", "age"),
draws = list(
numerator_nowcasted = numer,
denominator_nowcasted = denom
)
)
ens <- ens_add_rate(
ens,
numerator = "numerator_nowcasted",
denominator = "denominator_nowcasted",
per = 100
)
# the rate is a third draw matrix, named by the grammar
names(ens$draws)
#> [1] "numerator_nowcasted"
#> [2] "denominator_nowcasted"
#> [3] "numerator_nowcasted_vs_denominator_nowcasted_pr100"
# its interval carries the uncertainty of both measures
r <- ens_collapse(ens, probs = c(0.05, 0.5, 0.95))
r[, .(
isoyearweek,
lo = numerator_nowcasted_vs_denominator_nowcasted_pr100_q05x0,
med = numerator_nowcasted_vs_denominator_nowcasted_pr100_q50x0,
hi = numerator_nowcasted_vs_denominator_nowcasted_pr100_q95x0
)]
#> isoyearweek lo med hi
#> <char> <num> <num> <num>
#> 1: 2023-01 7.115385 9.755516 14.31502
#> 2: 2023-02 5.699153 9.867335 13.52267
#> 3: 2023-03 6.371382 9.476179 13.27110