Plot a gg_variable object,

Plot a gg_variable object,

Usage

# S3 method for class 'gg_variable'
plot(
  x,
  xvar,
  time,
  time_labels,
  panel = FALSE,
  oob = TRUE,
  points = TRUE,
  smooth = TRUE,
  ...
)

Arguments

x

gg_variable object created from a rfsrc object

xvar

variable (or list of variables) of interest.

time

For survival, one or more times of interest

time_labels

string labels for times

panel

Should plots be faceted along multiple xvar?

oob

oob estimates (boolean)

points

plot the raw data points (boolean)

smooth

include a smooth curve (boolean)

...

arguments passed to the ggplot2 functions.

Value

A single ggplot object, or list of ggplot objects

References

Breiman L. (2001). Random forests, Machine Learning, 45:5-32.

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

Ishwaran H. and Kogalur U.B. (2013). Random Forests for Survival, Regression and Classification (RF-SRC), R package version 1.4.

Examples

## ------------------------------------------------------------
## classification
## ------------------------------------------------------------
## -------- iris data
set.seed(42)
rfsrc_iris <- rfsrc(Species ~ ., data = iris, ntree = 50)

gg_dta <- gg_variable(rfsrc_iris)
plot(gg_dta, xvar = "Sepal.Width")

plot(gg_dta, xvar = "Sepal.Length")


## Panel plot across all predictors
plot(gg_dta,
  xvar = rfsrc_iris$xvar.names,
  panel = TRUE, se = FALSE
)
#> Warning: Ignoring unknown parameters: `se`


## ------------------------------------------------------------
## regression
## ------------------------------------------------------------
## -------- air quality data
# na.action = "na.impute" handles missing Ozone / Solar.R values
set.seed(42)
rfsrc_airq <- rfsrc(Ozone ~ ., data = airquality,
                    na.action = "na.impute", ntree = 50)
gg_dta <- gg_variable(rfsrc_airq)

# Treat Month as an ordinal factor for better visualisation
gg_dta[, "Month"] <- factor(gg_dta[, "Month"])

plot(gg_dta, xvar = "Wind")
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'

plot(gg_dta, xvar = "Temp")
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'

plot(gg_dta, xvar = "Solar.R")
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
#> Warning: Removed 7 rows containing non-finite outside the scale range (`stat_smooth()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_point()`).


# Panel plot across continuous predictors
plot(gg_dta, xvar = c("Solar.R", "Wind", "Temp", "Day"), panel = TRUE)
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
#> Warning: Removed 7 rows containing non-finite outside the scale range (`stat_smooth()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_point()`).


# Factor variable uses notched boxplots
plot(gg_dta, xvar = "Month", notch = TRUE)
#> Warning: Ignoring unknown parameters: `notch`
#> Notch went outside hinges
#> ℹ Do you want `notch = FALSE`?


## ------------------------------------------------------------
## survival examples
## ------------------------------------------------------------
## -------- veteran data
data(veteran, package = "randomForestSRC")
set.seed(42)
rfsrc_veteran <- rfsrc(Surv(time, status) ~ ., veteran,
  nsplit = 10,
  ntree = 50
)

# Marginal survival at 90 days
gg_dta <- gg_variable(rfsrc_veteran, time = 90)

# Single-variable dependence plots
plot(gg_dta, xvar = "age")
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'

plot(gg_dta, xvar = "diagtime")
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'


# Panel coplot for two predictors at a single time
plot(gg_dta, xvar = c("age", "diagtime"), panel = TRUE)
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'


# Compare survival at 30, 90, and 365 days simultaneously
gg_dta <- gg_variable(rfsrc_veteran, time = c(30, 90, 365))

# Single-variable plot (one facet per time point)
plot(gg_dta, xvar = "age")
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'


# Panel coplot across two predictors and three time points
plot(gg_dta, xvar = c("age", "diagtime"), panel = TRUE)
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'