Description Usage Arguments Details Value Author(s) References Examples
Run bart
at test observations constructed so that
a plot can be created
displaying the effect of
a single variable (pdbart
) or pair of variables (pd2bart
).
Note that if y is a binary with P(Y=1  x) = F(f(x)), F the standard
normal cdf, then the plots are all on the f scale.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23  pdbart(x.train, y.train,
xind = NULL,
levs = NULL, levquants = c(0.05, seq(0.1, 0.9, 0.1), 0.95),
pl = TRUE, plquants = c(0.05, 0.95),
...)
## S3 method for class 'pdbart'
plot(x,
xind = seq_len(length(x$fd)),
plquants = c(0.05, 0.95), cols = c('black', 'blue'),
...)
pd2bart(x.train, y.train,
xind = NULL,
levs = NULL, levquants = c(0.05, seq(0.1, 0.9, 0.1), 0.95),
pl = TRUE, plquants = c(0.05, 0.95),
...)
## S3 method for class 'pd2bart'
plot(x,
plquants = c(0.05, 0.95), contour.color = 'white',
justmedian = TRUE,
...)

x.train 
Explanatory variables for training (in sample) data. Can be any valid input to 
y.train 
Dependent variable for training (in sample) data. Can be a numeric vector or, when passing

xind 
Integer, character vector, or the righthand side of a formula indicating which variables are to be
plotted. In 
levs 
Gives the values of a variable at which the plot is to be constructed.
Must be a list, where the ith component gives the values for the ith variable.
In 
levquants 
If 
pl 
For 
plquants 
In the plots, beliefs about f(x) are indicated by plotting the
posterior median and a lower and upper quantile.

... 
Additional arguments.
In 
x 
For 
cols 
Vector of two colors. The first color is for the median of f, while the second color is for the upper and lower quantiles. 
contour.color 
Color for contours plotted on top of the image. 
justmedian 
A logical where if 
We divide the predictor vector x into a subgroup of interest, x_s and the complement x_c = x  x_s. A prediction f(x) can then be written as f(x_s, x_c). To estimate the effect of x_s on the prediction, Friedman suggests the partial dependence function
f_s(x_s) = (1/n) ∑_{i=1}\^n f(x_s,x_{ic})
where x_{ic} is the ith observation of x_c in the data. Note that (x_s, x_{ic}) will generally not be one of the observed data points. Using BART it is straightforward to then estimate and even obtain uncertainty bounds for f_s(x_s). A draw of f*_s(x_s) from the induced BART posterior on f_s(x_s) is obtained by simply computing f*_s(x_s) as a byproduct of each MCMC draw f*. The median (or average) of these MCMC draws f*_s(x_s) then yields an estimate of f_s(x_s), and lower and upper quantiles can be used to obtain intervals for f_s(x_s).
In pdbart
x_s consists of a single variable in x and in
pd2bart
it is a pair of variables.
This is a computationally intensive procedure.
For example, in pdbart
, to compute the partial dependence plot
for 5 x_s values, we need
to compute f(x_s, x_c) for all possible (x_s, x_{ic}) and there
would be 5n of these where n is the sample size.
All of that computation would be done for each kept BART draw.
For this reason running BART with keepevery
larger than 1 (eg. 10)
makes the procedure much faster.
The plot methods produce the plots and don't return anything.
pdbart
and pd2bart
return lists with components
given below. The list returned by pdbart
is assigned class
pdbart
and the list returned by pd2bart
is assigned
class pd2bart
.
fd 
A matrix whose (i, j) value is the ith draw of f_s(x_s) for the jth value of x_s. “fd” is for “function draws”. For For 
levs 
The list of levels used, each component corresponding to a variable.
If argument 
xlbs 
A vector of character strings which are the plotting labels used for the variables. 
The remaining components returned in the list are the same as in the value of bart
.
They are simply passed on from the BART run used to create the partial dependence plot.
The function plot.bart
can be applied to the object returned by pdbart
or
pd2bart
to examine the BART run.
Hugh Chipman: [email protected].
Robert McCulloch: [email protected].
Chipman, H., George, E., and McCulloch, R. (2006) BART: Bayesian Additive Regression Trees.
Chipman, H., George, E., and McCulloch R. (2006) Bayesian Ensemble Learning.
both of the above at: http://www.robmcculloch.org/
Friedman, J.H. (2001) Greedy function approximation: A gradient boosting machine. The Annals of Statistics, 29, 1189–1232.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47  ## Not run:
## simulate data
f < function(x) { return(0.5 * x[,1] + 2 * x[,2] * x[,3]) }
sigma < 0.2
n < 100
set.seed(27)
x < matrix(2 * runif(n * 3) 1, ncol = 3)
colnames(x) < c('rob', 'hugh', 'ed')
Ey < f(x)
y < rnorm(n, Ey, sigma)
## first two plot regions are for pdbart, third for pd2bart
par(mfrow = c(1, 3))
## pdbart: one dimensional partial dependence plot
set.seed(99)
pdb1 <
pdbart(x, y, xind = c(1, 2),
levs = list(seq(1, 1, 0.2), seq(1, 1, 0.2)),
pl = FALSE, keepevery = 10, ntree = 100)
plot(pdb1, ylim = c(0.6,.6))
## pd2bart: two dimensional partial dependence plot
set.seed(99)
pdb2 <
pd2bart(x, y, xind = c(2, 3),
levquants = c(0.05, 0.1, 0.25, 0.5, 0.75, 0.9, 0.95),
pl = FALSE, ntree = 100, keepevery = 10, verbose = FALSE)
plot(pdb2)
## compare BART fit to linear model and truth = Ey
lmFit < lm(y ~., data.frame(x, y))
fitmat < cbind(y, Ey, lmFit$fitted, pdb1$yhat.train.mean)
colnames(fitmat) < c('y', 'Ey', 'lm', 'bart')
print(cor(fitmat))
## example showing the use of a prefitted model
df < data.frame(y, x)
set.seed(99)
bartFit < bart(y ~ rob + hugh + ed, df,
keepevery = 10, ntree = 100, keeptrees = TRUE)
pdb1 < pdbart(bartFit, xind = rob + ed, pl = FALSE)
## End(Not run)

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