rfvimptest (version 0.1.3)

allinone: Apply all available (sequential) permutation testing approaches of variable importance measures with one function call

Description

This is a helper function, which allows to perform all (sequential) permutation testing approaches of variable importance measures described in rfvimptest with a single function call. This may be useful for comparing the results obtained using the different approaches. Importantly, this function is computationally efficient by re-using the permuted variable importance values obtained for the conventional permutation test (that performs all Mmax permutations) for the other approaches. For details on the different approaches see rfvimptest.

Usage

allinone(
  data,
  yname,
  Mmax = 500,
  varnames = NULL,
  p0 = 0.06,
  p1 = 0.04,
  alpha = 0.05,
  beta = 0.2,
  A = 0.1,
  B = 10,
  h = 8,
  nperm = 1,
  ntree = 500,
  progressbar = TRUE,
  condinf = FALSE,
  ...
)

Value

Object of class allinone with elements

varimp

Variable importance for each considered independent variable.

testres

The results ("keep H0" vs. "accept H1") of the tests for each considered independent variable.

pvalues

The p-values of the tests for each considered independent variable. Note that p-values are only obtained for the method types "pval" and "complete".

stoppedearly

For each independent variable, whether the calculations stopped early ("yes") or the maximum of Mmax permutations was reached ("no").

perms

The number of permutations performed for each independent variable.

Mmax

Maximum number of permutations used in each permutation test.

ntree

Number of trees per forest.

comptime

The time the computations needed.

Arguments

data

A data.frame containing the variables in the model.

yname

Name of outcome variable.

Mmax

Maximum number of permutations used in each permutation test. Default is 500.

varnames

Optional. Names of the variables for which testing should be performed. By default all variables in data with the exception of the outcome variable are used.

p0

The value of the p-value in the null hypothesis (H0: p = p0) of SPRT and SAPT. Default is 0.06.

p1

The value of the p-value in the alternative hypothesis (H1: p = p1) of SPRT and SAPT. Default is 0.04.

alpha

The significance level of SPRT when p = p0. Also known as type I error. Default is 0.05.

beta

One minus the power of SPRT when p = p1. Also known as type II error. Default is 0.2.

A

The quantity A in the formula of SAPT. Default is 0.1 for a type I error of 0.05. Usually not changed by the user.

B

The quantity B in the formula of SAPT. Default is 10 (1/A) for a type I error of 0.05. Usually not changed by the user.

h

The quantity h in the formula for the sequential Monte Carlo p-value. The default value for h is 8. Larger values lead to more precise p-value estimates, but are computationally more expensive.

nperm

The numbers of permutations of the out-of-bag observations over which the results are averaged, when calculating the variable importance measure values. Default is 1. Larger values than 1 can only be considered when condinf=TRUE, that is, when using random forests with conditional inference trees (Hothorn et al., 2006) as base learners.

ntree

Number of trees per forest. Default is 500.

progressbar

Output the current progress of the calculations for each variable to the console? Default is TRUE.

condinf

Set this value to TRUE if random forests using conditional inference trees (Hothorn et al., 2006) should be used and to FALSE if classical random forests using CART trees should be used. Default is FALSE.

...

Further arguments passed to ranger::ranger (if condinf=FALSE) or
party::cforest_unbiased() (if condinf=TRUE).

Author

Alexander Hapfelmeier, Roman Hornung

References

• Breiman, L. (2001). Random forests. Mach Learn, 45:5-32, <tools:::Rd_expr_doi("10.1023/A:1010933404324")>.

• Coleman, T., Peng, W., Mentch, L. (2019). Scalable and efficient hypothesis testing with random forests. arXiv preprint arXiv:1904.07830, <tools:::Rd_expr_doi("10.48550/arXiv.1904.07830")>.

• Hapfelmeier, A., Hornung, R., Haller, B. (2022). Sequential Permutation Testing of Random Forest Variable Importance Measures. arXiv preprint arXiv:2206.01284, <tools:::Rd_expr_doi("10.48550/arXiv.2206.01284")>.

• Hapfelmeier, A., Ulm, K. (2013). A new variable selection approach using Random Forests. CSDA 60:50–69, <tools:::Rd_expr_doi("10.1016/j.csda.2012.09.020")>.

• Hapfelmeier, A., Hothorn, T., Ulm, K., Strobl, C. (2014). A new variable importance measure for random forests with missing data. Stat Comput 24:21–34, <tools:::Rd_expr_doi("10.1007/s11222-012-9349-1")>.

• Hothorn, T., Hornik, K., Zeileis, A. (2006). Unbiased Recursive Partitioning: A Conditional Inference Framework. J Comput Graph Stat 15(3):651–674, <tools:::Rd_expr_doi("10.1198/106186006X133933")>.

• Wright, M. N., Ziegler, A. (2017). ranger: A fast implementation of random forests for high dimensional data in C++ and R. J Stat Softw 77:1-17, <tools:::Rd_expr_doi("10.18637/jss.v077.i01")>.

See Also

rfvimptest

Examples

# \donttest{

# Load package:
library("rfvimptest")

# Set seed to obtain reproducible results:
set.seed(1234)

# Load example data:
data(hearth2)

# NOTE: For illustration purposes very small numbers of maximum
# permutations are considered in the below examples.
# This number would be much too small for actual applications.
# The default number is Max=500.

# When using condinf=FALSE (default) the results for the two-sample
# permutation tests are not obtained:
(ptest <- allinone(data=hearth2, yname="Class",  Mmax=20))

# Variable importance values with p-values from the Monte Carlo p-value
# and the complete approach:
ptest$varimp
ptest$pvalues$pval
ptest$pvalues$complete


# When setting condinf=TRUE the results are obtained for all approaches,
# that is, including those for the two-sample permutation tests
# (in this illustration very small number of trees ntree=30 are used,
# in practice much larger numbers should be used; the default is ntree=500):
(ptest_ci <- allinone(data=hearth2, yname="Class", condinf=TRUE, ntree=30, Mmax=10))
ptest_ci$testres

# }