partial_surface_data: Cached `plot.variable` objects for examples, diagnostics and vignettes. Data sets storing `plot.variable` objects corresponding to training data according to the following naming convention:

`partial_boston_surf` - from a randomForestS[R]C for the `Boston` housing data set (`MASS` package).

`partial_pbc_surf` - from a randomForest[S]RC for the `pbc` data set (`randomForestSRC` package)

`partial_pbc_time` - from a randomForest[S]RC for the `pbc` data set (`randomForestSRC` package)

Description

Cached plot.variable objects for examples, diagnostics and vignettes.

Data sets storing plot.variable objects corresponding to training data according to the following naming convention:

partial_boston_surf - from a randomForestS[R]C for the Boston housing data set (MASS package).
partial_pbc_surf - from a randomForest[S]RC for the pbc data set (randomForestSRC package)
partial_pbc_time - from a randomForest[S]RC for the pbc data set (randomForestSRC package)

Arguments

Format

list of plot.variable objects

Details

Constructing partial plot data with the randomForestSRC::plot.variable function are computationally expensive. We cache plot.variable objects to improve the ggRandomForests examples, diagnostics and vignettes run times. (see cache_rfsrc_datasets to rebuild a complete set of these data sets.)

For each data set listed, we build a rfsrc (see rfsrc_data), then calculate the partial plot data with plot.variable function, setting partial=TRUE. Each data set is built with the cache_rfsrc_datasets with the randomForestSRC version listed in the ggRandomForests DESCRIPTION file.

partial_boston - The Boston housing values in suburbs of Boston from the MASS package. Build a regression random forest for predicting medv (median home values) on 13 covariates and 506 observations.
partial_pbc - The pbc data from the Mayo Clinic trial in primary biliary cirrhosis (PBC) of the liver conducted between 1974 and 1984. A total of 424 PBC patients, referred to Mayo Clinic during that ten-year interval, met eligibility criteria for the randomized placebo controlled trial of the drug D-penicillamine. 312 cases participated in the randomized trial and contain largely complete data. Data from the randomForestSRC package. Build a survival random forest for time-to-event death data with 17 covariates and 312 observations (remaining 106 observations are held out).

References

#--------------------- randomForestSRC ---------------------

Ishwaran H. and Kogalur U.B. (2014). Random Forests for Survival, Regression and Classification (RF-SRC), R package version 1.5.5.

Ishwaran H. and Kogalur U.B. (2007). Random survival forests for R. R News 7(2), 25-31.

Ishwaran H., Kogalur U.B., Blackstone E.H. and Lauer M.S. (2008). Random survival forests. Ann. Appl. Statist. 2(3), 841-860.

#--------------------- Boston data set ---------------------

Belsley, D.A., E. Kuh, and R.E. Welsch. 1980. Regression Diagnostics. Identifying Influential Data and Sources of Collinearity. New York: Wiley.

Harrison, D., and D.L. Rubinfeld. 1978. "Hedonic Prices and the Demand for Clean Air." J. Environ. Economics and Management 5: 81-102.

#--------------------- pbc data set ---------------------

Fleming T.R and Harrington D.P., (1991) Counting Processes and Survival Analysis. New York: Wiley.

T Therneau and P Grambsch (2000), Modeling Survival Data: Extending the Cox Model, Springer-Verlag, New York. ISBN: 0-387-98784-3.

Examples

Run this code

if (FALSE) {
#---------------------------------------------------------------------
# MASS::Boston data - regression random forest 
#---------------------------------------------------------------------
# load the rfsrc object from the cached data
data(rfsrc_boston, package="ggRandomForests")

# The plot.variable call
partial_boston <- plot.variable(rfsrc_boston,
                                partial=TRUE, show.plots = FALSE )

# plot the forest partial plots
gg_dta <- gg_partial(partial_boston)
plot(gg_dta, panel=TRUE)

#---------------------------------------------------------------------
# randomForestSRC::pbc data - survival random forest
#---------------------------------------------------------------------
# load the rfsrc object from the cached data
data(rfsrc_pbc, package="ggRandomForests")

# Restrict the time of interest to less than 5 years.
time_pts <- rfsrc_pbc$time.interest[which(rfsrc_pbc$time.interest<=5)]

# Find the 50 points in time, evenly space along the distribution of 
# event times for a series of partial dependence curves
time_cts <-quantile_pts(time_pts, groups = 50)

# Generate the gg_partial_coplot data object
system.time(partial_pbc_time <- lapply(time_cts, function(ct) {
   plot.variable(rfsrc_pbc, xvar = "bili", time = ct,
                 npts = 50, show.plots = FALSE, 
                 partial = TRUE, surv.type="surv")
   }))
#     user   system  elapsed 
# 2561.313   81.446 2641.707 

# Find the quantile points to create 50 cut points
alb_partial_pts <-quantile_pts(rfsrc_pbc$xvar$albumin, groups = 50)

system.time(partial_pbc_surf <- lapply(alb_partial_pts, function(ct) {
  rfsrc_pbc$xvar$albumin <- ct
  plot.variable(rfsrc_pbc, xvar = "bili", time = 1,
                npts = 50, show.plots = FALSE, 
                partial = TRUE, surv.type="surv")
  }))
# user   system  elapsed 
# 2547.482   91.978 2671.870 

}