| gp {brms} | R Documentation |
Function used to set up a Gaussian process term in brms. The function does not evaluate its arguments – it exists purely to help set up a model with Gaussian process terms.
gp(..., by = NA, cov = "exp_quad", gr = FALSE, scale = TRUE)
... |
One or more predictors for the Gaussian process. |
by |
A numeric or factor variable of the same length as each predictor. In the numeric vector case, the elements multiply the values returned by the Gaussian process. In the factor variable case, a separate Gaussian process is fitted for each factor level. |
cov |
Name of the covariance kernel. By default,
the exponentiated-quadratic kernel |
gr |
Logical; Indicates if auto-grouping should be used (defaults
to |
scale |
Logical; If |
A Gaussian process is a stochastic process, which describes the relation between one or more predictors x = (x_1, ..., x_d) and a response f(x), where d is the number of predictors. A Gaussian process is the generalization of the multivariate normal distribution to an infinite number of dimensions. Thus, it can be interpreted as a prior over functions. Any finite sample realized from this stochastic process is jointly multivariate normal, with a covariance matrix defined by the covariance kernel k_p(x), where p is the vector of parameters of the Gaussian process:
f(x) ~ MVN(0, k_p(x))
The smoothness and general behavior of the function f depends only on the choice of covariance kernel. For a more detailed introduction to Gaussian processes, see https://en.wikipedia.org/wiki/Gaussian_process.
Below, we describe the currently supported covariance kernels:
"exp_quad": The exponentiated-quadratic kernel is defined as k(x_i, x_j) = sdgp^2 exp(- || x_i - x_j || / (2 lscale^2)), where || . || is the Euclidean norm, sdgp is a standard deviation parameter, and lscale is characteristic length-scale parameter. The latter practically measures how close two points x_i and x_j have to be to influence each other substantially.
In the current implementation, "exp_quad" is the only supported
covariance kernel. More options will follow in the future.
An object of class 'gpterm', which is a list
of arguments to be interpreted by the formula
parsing functions of brms.
## Not run: # simulate data using the mgcv package dat <- mgcv::gamSim(1, n = 30, scale = 2) # fit a simple gaussian process model fit1 <- brm(y ~ gp(x2), dat, chains = 2) summary(fit1) me1 <- marginal_effects(fit1, nsamples = 200, spaghetti = TRUE) plot(me1, ask = FALSE, points = TRUE) # fit a more complicated gaussian process model fit2 <- brm(y ~ gp(x0) + x1 + gp(x2) + x3, dat, chains = 2) summary(fit2) me2 <- marginal_effects(fit2, nsamples = 200, spaghetti = TRUE) plot(me2, ask = FALSE, points = TRUE) # fit a multivariate gaussian process model fit3 <- brm(y ~ gp(x1, x2), dat, chains = 2) summary(fit3) me3 <- marginal_effects(fit3, nsamples = 200, spaghetti = TRUE) plot(me3, ask = FALSE, points = TRUE) # compare model fit LOO(fit1, fit2, fit3) # simulate data with a factor covariate dat2 <- mgcv::gamSim(4, n = 90, scale = 2) # fit separate gaussian processes for different levels of 'fac' fit4 <- brm(y ~ gp(x2, by = fac), dat2, chains = 2) summary(fit4) plot(marginal_effects(fit4), points = TRUE) ## End(Not run)