gp_opts {EpiNow2} | R Documentation |
Approximate Gaussian Process Settings
Description
Defines a list specifying the structure of the approximate Gaussian
process. Custom settings can be supplied which override the defaults.
Usage
gp_opts(
basis_prop = 0.2,
boundary_scale = 1.5,
ls_mean = 21,
ls_sd = 7,
ls_min = 0,
ls_max = 60,
alpha_sd = 0.05,
kernel = c("matern_3/2", "se"),
matern_type = 3/2
)
Arguments
basis_prop |
Numeric, proportion of time points to use as basis functions. Defaults to 0.2. Decreasing this value results in a decrease in accuracy but a faster compute time (with increasing it having the first effect). In general smaller posterior length scales require a higher proportion of basis functions. See (Riutort-Mayol et al. 2020 https://arxiv.org/abs/2004.11408) for advice on updating this default. |
boundary_scale |
Numeric, defaults to 1.5. Boundary scale of the approximate Gaussian process. See (Riutort-Mayol et al. 2020 https://arxiv.org/abs/2004.11408) for advice on updating this default. |
ls_mean |
Numeric, defaults to 21 days. The mean of the lognormal length scale. |
ls_sd |
Numeric, defaults to 7 days. The standard deviation of the log
normal length scale. If |
ls_min |
Numeric, defaults to 0. The minimum value of the length scale. |
ls_max |
Numeric, defaults to 60. The maximum value of the length
scale. Updated in |
alpha_sd |
Numeric, defaults to 0.05. The standard deviation of the magnitude parameter of the Gaussian process kernel. Should be approximately the expected standard deviation of the logged Rt. |
kernel |
Character string, the type of kernel required. Currently
supporting the squared exponential kernel ("se") and the 3 over 2 Matern
kernel ("matern", with |
matern_type |
Numeric, defaults to 3/2. Type of Matern Kernel to use. Currently only the Matern 3/2 kernel is supported. |
Value
A <gp_opts>
object of settings defining the Gaussian process
Examples
# default settings
gp_opts()
# add a custom length scale
gp_opts(ls_mean = 4)