BayesTreePrior (version 1.0.1)

BayesTreePriorNotOrthogonal: Simulation of the tree prior in the general case (Case #4).

Description

Generate $n_{iter}$ trees from the prior distribution in the general case (Case #4).

Usage

BayesTreePriorNotOrthogonal(alpha, beta, X, n_iter = 500, minpart = 1, pvars = NULL, MIA = FALSE, missingdummy = FALSE)

Arguments

alpha

base parameter of the tree prior, $\alpha \in [0,1)$.

beta

power parameter of the tree prior, $\beta \geq 0$.

X

data.frame of the design matrix.

n_iter

number of trees to generate, $n_{iter}>0$.

minpart

the minimum number of observations required in one of the child to be able to split, $minpart>0$.

pvars

vector of probabilities for the choices of variables to split (Will automatically be normalized so that the sum equal to 1). It must be twice as large as the number of variables when $missingdummy$ is TRUE.

MIA

set to TRUE if you want Missing Incorporated in Attributes (MIA) imputation to be used.

missingdummy

set to TRUE if you have dummy coded the NAs.

Value

Returns a list containing, in the following order: the mean number of bottom nodes, the standard deviation of the number of bottom nodes, the mean of the depth, the standard deviation of the depth and a data.frame of vectors $(b_i,d_i)$, where $b_i$ is the number of bottom nodes and $d_i$ is the depth of the $i$th generated tree ($i=1, \ldots ,n_{iter}$).

See Also

BayesTreePriorOrthogonalInf, BayesTreePriorOrthogonal

Examples

if (requireNamespace("MASS", quietly = TRUE)) {
    x1 = MASS::mcycle$times
    x1[sample(1:length(x1), 20)] <- NA
    x2= MASS::mcycle$accel
    x2[sample(1:length(x2), 20)] <- NA
    X = cbind(x1, x2)
    results1 = BayesTreePriorNotOrthogonal(.95,.5, data.frame(X), minpart=5)
    X_dummies = is.na(X) + 0
    results2 = BayesTreePriorNotOrthogonal(.95,.5, data.frame(cbind(X,X_dummies)), minpart=5, 
    MIA=TRUE, missingdummy=TRUE)
}