View source: R/custom_priors.R
custom_priors | R Documentation |
Priors can be specified in several ways in outbreaker2 (see details and examples). The most flexible way to specify a prior is to provide a prior function directly. This function must take an argument 'param', which is a list which contains all the states of the parameters and augmented data. See the documentation of create_param for more information.
custom_priors(...) ## S3 method for class 'custom_priors' print(x, ...)
... |
A list or a series of named, comma-separated functions implementing priors. Each function must have a single argument, which corresponds to a 'outbreaker_param' list. |
x |
an |
There are three ways a user can specify priors:
1) Default: this is what happens when the 'config' has default values of
prior parameters.
2) Customized parameters: in this case, the prior functions are the default
ones from the package, but will use custom parameters, specified by the user
through create_config
.
3) Customized functions: in this case, prior functions themselves are
specified by the user, through the '...' argument of 'custom_priors'. The
requirements is that such functions must have either hard-coded parameters or
enclosed values. They will take a single argument which is a list containing
all model parameters with the class 'outbreaker_param'. ALL PRIORS functions
are expected to return values on a LOG SCALE.
Priors currently used for the model are:
mu
(mutation rate): default function is an exponential
distribution implemented in outbreaker:::cpp_prior_mu
. New prior
functions should use x$mu
to refer to the current value of mu
,
assuming their argument is called x
.
pi
(reporting probability): default function is a beta
distribution implemented in outbreaker:::cpp_prior_pi
. New prior
functions should use x$pi
to refer to the current value of pi
,
assuming their argument is called x
.
eps
(contact reporting coverage): default function is a beta
distribution implemented in outbreaker:::cpp_prior_eps
. New prior
functions should use x$eps
to refer to the current value of eps
,
assuming their argument is called x
.
lambda
(non-infectious contact rate): default function is a
beta distribution implemented in outbreaker:::cpp_prior_lambda
. New
prior functions should use x$lambda
to refer to the current value of
lambda
, assuming their argument is called x
.
A list of custom functions with class custom_priors
. Values
set to NULL
will be ignored and default functions will be used
instead.
Thibaut Jombart (thibautjombart@gmail.com).
See customization vignette for detailed examples on how to customize priors.
## BASIC CONFIGURATION custom_priors() ## SPECIFYING PRIOR PARAMETERS ## - this will need to be passed to outbreaker default_config <- create_config() new_config <- create_config(prior_mu = 1e-5, prior_pi = c(2, 1)) ## - to check the prior manually, default settings: param <- list(mu = 0.001, pi = 0.9) outbreaker2:::cpp_prior_mu(param, default_config) outbreaker2:::cpp_prior_pi(param, default_config) outbreaker2:::cpp_prior_mu(param, new_config) outbreaker2:::cpp_prior_pi(param, new_config) ## these correspond to: dexp(0.001, 0.01, log = TRUE) dbeta(0.9, 2, 1, log = TRUE) ## SPECIFYING A PRIOR FUNCTION ## flat prior for pi between 0.5 and 1 f <- function(x) {ifelse(x$pi > 0.5, log(2), log(0))} priors <- custom_priors(pi = f) priors # this should be passed to outbreaker ## test the prior manually priors$pi(list(pi=1)) priors$pi(list(pi=.6)) priors$pi(list(pi=.2)) priors$pi(list(pi=.49))
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