vivid: pdpVars – R documentation

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pdpVars

Description

Displays the individual conditional expectation (ICE) curves and aggregated partial dependence for each variable in a grid.

Usage

pdpVars(
  data,
  fit,
  response,
  vars = NULL,
  pal = rev(RColorBrewer::brewer.pal(11, "RdYlBu")),
  gridSize = 10,
  nmax = 500,
  class = 1,
  nIce = 30,
  predictFun = NULL,
  limits = NULL,
  colorVar = NULL,
  draw = TRUE
)

Arguments

`data`	Data frame used for fit.
`fit`	A supervised machine learning model, which understands condvis2::CVpredict
`response`	The name of the response for the fit.
`vars`	The variables to plot (and their order), defaults to all variables other than response.
`pal`	A vector of colors to show predictions, for use with scale_fill_gradientn
`gridSize`	The size of the grid for evaluating the predictions.
`nmax`	Uses sample of nmax data rows for the pdp. Use all rows if NULL.
`class`	Category for classification, a factor level, or a number indicating which factor level.
`nIce`	Number of ice curves to be plotted, defaults to 30.
`predictFun`	Function of (fit, data) to extract numeric predictions from fit. Uses condvis2::CVpredict by default, which works for many fit classes.
`limits`	A vector determining the limits of the predicted values.
`colorVar`	Which variable to colour the predictions by.
`draw`	If FALSE, then the plot will not be drawn. Default is TRUE.

Value

A grid displaying ICE curves and univariate partial dependence.

Examples

# Load in the data:
aq <- na.omit(airquality)
fit <- lm(Ozone ~ ., data = aq)
pdpVars(aq, fit, "Ozone")

# Classification
library(ranger)
rfClassif <- ranger(Species ~ ., data = iris, probability = TRUE)
pdpVars(iris, rfClassif, "Species", class = 3)

pp <- pdpVars(iris, rfClassif, "Species", class = 2, draw = FALSE)
pp[[1]]
pdpVars(iris, rfClassif, "Species", class = 2, colorVar = "Species")

vivid

Variable Importance and Variable Interaction Displays

v0.1.0

GPL (>= 2)

Authors

Alan Inglis [aut, cre], Andrew Parnell [aut], Catherine Hurley [aut]

Initial release