Defines the parameters of a supported distribution for use in onward
modelling. Multiple distribution families are supported - see the
documentation for
family
for details. Alternatively, a nonparametric
distribution can be specified using the pmf
argument.
This function provides distribution
functionality in delay_opts()
, generation_time_opts()
, and
trunc_opts()
.
Arguments
- mean
Numeric. If the only non-zero summary parameter then this is the fixed interval of the distribution. If the
sd
is non-zero then this is the mean of the distribution given bydist
. If this is not given a vector of empty vectors is returned.- sd
Numeric, defaults to 0. Sets the standard deviation of the distribution.
- mean_sd
Numeric, defaults to 0. Sets the standard deviation of the uncertainty around the mean of the distribution assuming a normal prior.
- sd_sd
Numeric, defaults to 0. Sets the standard deviation of the uncertainty around the sd of the distribution assuming a normal prior.
- distribution
Character, defaults to "lognormal". The (discretised distribution to be used. If sd == 0 then the distribution is fixed and a delta function is used. If sd > 0 then the distribution is discretised and truncated.
The following distributions are currently supported:
"lognormal" - a lognormal distribution. For this distribution
mean
is the mean of the natural logarithm of the delay (on the log scale) andsd
is the standard deviation of the natural logarithm of the delay."gamma" - a gamma distribution. For this distribution
mean
is the mean of the delay andsd
is the standard deviation of the delay. During model fitting these are then transformed to the shape and scale of the gamma distribution.
When
distribution
is the default lognormal distribution the other function arguments have the following definition:mean
is the mean of the natural logarithm of the delay (on the log scale).sd
is the standard deviation of the natural logarithm of the delay.
- max
Numeric, maximum value of the distribution. The distribution will be truncated at this value.
- pmf
Numeric, a vector of values that represent the (nonparametric) probability mass function of the delay (starting with 0); defaults to an empty vector corresponding to a parametric specification of the distribution (using
mean
,sd
and corresponding uncertainties)- fixed
Logical, defaults to
FALSE
. Should delays be treated as coming from fixed (vs uncertain) distributions. Overrides any values assigned tomean_sd
andsd_sd
by setting them to zero. reduces compute requirement but may produce spuriously precise estimates.
Examples
# A fixed lognormal distribution with mean 5 and sd 1.
dist_spec(mean = 5, sd = 1, max = 20, distribution = "lognormal")
#>
#> Fixed distribution with PMF [1.3e-05 0.00035 0.0018 0.0046 0.0088 0.014 0.02 0.027 0.035 0.043 0.051 0.058 0.066 0.074 0.082 0.089 0.096 0.1 0.11 0.12]
#>
# An uncertain gamma distribution with mean 3 and sd 2
dist_spec(
mean = 3, sd = 2, mean_sd = 0.5, sd_sd = 0.5, max = 20,
distribution = "gamma"
)
#>
#> Uncertain gamma distribution with (untruncated) mean 3 (SD 0.5) and SD 2 (SD 0.5)
#>