plot_ALE_multi: Plots Accumulated Local Effects for ERF for multivariate...

In zsiders/EnsembleRandomForests: Ensemble Random Forests

Plots Accumulated Local Effects for ERF for multivariate factors

Description

Plots the Accumulated Local Effects (ALE) from an ERF object

Usage

plot_ALE_multi(
  ALE,
  xquantiles = c(0.025, 0.975),
  yquantiles = c(0.1, 0.5, 0.9),
  name,
  cex.axis = 1,
  cex.lab = 1,
  rug = TRUE,
  rug.col = "gray50",
  xaxs = TRUE,
  gap.axis = NA,
  rug.tick = 0.02,
  rug.lwd = 0.5,
  rug.alpha = 0.2,
  rug.max = 1000,
  poly.colp = c("#fcde9c", "#e34f6f", "#7c1d6f"),
  poly.alpha = 0.5,
  level.names
)

Arguments

ALE	an ALE object for a given variable; indexed as a list for full functionality
xquantiles	lower and upper quantile bounds to limit x values to
yquantiles	lower, middle, and upper quantiles to plot the confidence interval around the ALE predictions
name	the x-axis label of the variable; self-supplied if indexed as a list
cex.axis	the cex of the axis
cex.lab	the cex of the labels
rug	logical for turning the rug plot on/off (defaults to table values for class=='factor')
rug.col	color of rug ticks
rug.tick	length of rug ticks
rug.lwd	width of rug ticks
rug.alpha	transparency of rug ticks
rug.max	maximum number of ticks to plot (useful for big data)
poly.colp	is a vector of colors equal to n levels in response metric
poly.alpha	is a transparency value between 0 and 1 for the confidence interval polygon from the ERF predictions
level.names	names of the multivariate levels

Value

A plot of the ALEs

Examples

#run an ERF with 10 RFs and 
logit <- function(x){log(x/(1-x))}
inv_logit <- function(x){exp(x)/(exp(x)+1)}

x_mat <- as.data.frame(replicate(4, rnorm(1e4)))
x_mat_bin <- t(rmultinom(1e4,1,prob=c(0.33,0.33,0.33)))
x_mat$V5 <- factor(apply(x_mat_bin,1,function(x)which(x==1)))

y_gin <- function(){
	eff <- rnorm(ncol(x_mat)-1)
eff_bin <- rnorm(ncol(x_mat_bin))
y_logit <- t(eff %*% t(x_mat[,-5])) + t(eff_bin %*% t(x_mat_bin))
y <- inv_logit(y_logit)
return(y)
}

y_poss <- data.frame(y1 = y_gin(),
                    y2 = y_gin(),
                    y3 = y_gin())

y_bin <- apply(y_poss,1,function(x) rmultinom(1,1,x))
y <- apply(y_bin,2,function(x)which(x==1))
df <- data.frame(y = factor(y),x_mat)

ens_rf_ex <- ens_random_forests(df=df, var="obs", covariates=colnames(df[,-1]), save=FALSE, cores=1)


ALE_df <- ALE_fn(ens_rf_ex, save=FALSE, multi=TRUE, type='prob')

plot_ALE_multi(ALE_df[1])

zsiders/EnsembleRandomForests documentation built on Oct. 8, 2024, 11:41 p.m.