jmpost settings

Define settings that modify the behaviour of the jmpost package

Each of the following are the name of options that can be set via:

options(<option_name> = <value>)

jmpost.prior_shrinkage

Default = 0.5

By default all initial values are drawn as random sample from the respective prior distribution with a shrinkage factor towards the mean. That is:

initial_value = prior_mean * prior_shrinkage + (1 - prior_shrinkage) * prior_sample

This setting controls the shrinkage factor. A value of 0 means no shrinkage (i.e. pure random draw) whilst a value of 1 means the initial value is just the mean.

jmpost.cache_dir

Default = tempfile()

Directory to store compiled stan models in. If not set, a temporary directory is used for the given R session. Can also be set via the environment variable JMPOST_CACHE_DIR.

jmpost.gauss_quad_n

Default = 15

In most cases the survival function of the joint model does not have a closed form and as such it is calculated by integrating the hazard function. jmpost estimates this via Gaussian Quadrature, in particular it uses statmod::gauss.quad with kind = "legendre" to create the nodes and weights.

This option specifies the n argument in the call to statmod::gauss.quad. In general higher values of n lead to better accuracy of the approximation but at the cost of increased computational time.

Usage

set_options()

Examples

if (FALSE) {
options(jmpost.prior_shrinkage = 0.5)
}