gp_opts | R Documentation |
Defines a list specifying the structure of the approximate Gaussian process. Custom settings can be supplied which override the defaults.
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", "se", "ou"),
matern_order = 3/2,
matern_type
)
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", or "matern" with
'matern_order = Inf'), 3 over 2 oder 5 over 2 Matern kernel ("matern", with
|
matern_order |
Numeric, defaults to 3/2. Order of Matérn Kernel to use. Currently the orders 1/2, 3/2, 5/2 and Inf are supported. |
matern_type |
Deprated; Numeric, defaults to 3/2. Order of Matérn Kernel to use. Currently the orders 1/2, 3/2, 5/2 and Inf are supported. |
A <gp_opts>
object of settings defining the Gaussian process
# default settings
gp_opts()
# add a custom length scale
gp_opts(ls_mean = 4)
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