Skip to contents

Estimate a 2D potential landscape from data with the MVKE method

Source: R/2d_landscape.R
fit_2d_ld.Rd

This function is a wrapper of the MVKE method (see MVKE()) that produces a 2D potential landscape from 1D data. The landscape is constructed by estimating the gradient of the data and then integrating it. The MVKE method is a non-parametric method that estimates the gradient of the data by using a kernel density estimator. The potential landscape is then constructed by integrating the gradient.

Usage

fit_2d_ld(
  data,
  x,
  lims,
  n = 200L,
  vector_position = "start",
  na_action = "omit_data_points",
  method = c("MVKE"),
  subdivisions = 100L,
  rel.tol = .Machine$double.eps^0.25,
  abs.tol = rel.tol,
  stop.on.error = TRUE,
  keep.xy = FALSE,
  aux = NULL,
  ...
)

# S3 method for class '`2d_MVKE_landscape`'
summary(object, ...)

Arguments

data

A data frame or matrix containing the data. The data frame should contain at least a column, with the column name indicated by x, that represents the dimension for landscape construction.

x

The column name of the data frame that represents the dimension for landscape construction.

lims

The limits of the range for the landscape calculation as c(xl, xu).

n

The number of equally spaced points in the axis, at which the landscape is to be estimated.

vector_position

One of "start", "middle", or "end", representing the position of the vectors. If "start", for example, the starting point of a vector is regarded as the position of the vector.

na_action

One of "omit_data_points" or "omit_vectors". If using "omit_data_points", then only the NA points are omitted, and the points before and after an NA will form a vector. If using "omit_vectors", then the vectors will be omitted if either of its points is NA.

method

The method used to estimate the gradient. Currently only "MVKE" is supported.

subdivisions

the maximum number of subintervals.

rel.tol

relative accuracy requested.

abs.tol

absolute accuracy requested.

stop.on.error

logical. If true (the default) an error stops the function. If false some errors will give a result with a warning in the message component.

keep.xy

unused. For compatibility with S.

aux

unused. For compatibility with S.

...

Not used.

object

An object of class 2d_MVKE_landscape returned by fit_2d_ld().

Value

A 2d_MVKE_landscape object, which contains the following components:

  • dist: A data frame containing the estimated potential landscape. The data frame has two columns: x and U, where x is the position and U is the potential.

  • p: A ggplot object containing the plot of the potential landscape.

Functions

  • summary(`2d_MVKE_landscape`): Find the local minima of the 2D potential landscape

Examples

# generate data
single_output_grad <- simlandr::sim_fun_grad(length = 200, seed = 1614)
# fit the landscape
l <- fit_2d_ld(single_output_grad, "x")

summary(l)
#> 2 local minima were found.
#>            x          U
#> 1 -0.8310960 -0.2371366
#> 2  0.6845536 -0.1698856
plot(l)


# different behaviors for different `na_action` choices

l1 <- fit_2d_ld(data.frame(x = c(1,2,1,2,NA,NA,NA,10,11,10,11)), "x")
#> NA(s) found in the data. Those data points were omitted.
plot(l1)


l2 <- fit_2d_ld(data.frame(x = c(1,2,1,2,NA,NA,NA,10,11,10,11)), "x", na_action = "omit_vectors")
#> NA(s) found in the data. Those vectors were omitted.
plot(l2)