Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Genuer, R. and Poggi, J.M. and Tuleau-Malot, C. (2015)
< https://journal.r-project.org/archive/2015-2/genuer-poggi-tuleaumalot.pdf>.
News
News about the R package VSURF:
Main changes in Version 1.0.4 (2018-04-09)
skip all tests because randomForest package is being updated and behavior
with set.seed() is changing (and hence crashing all tests of VSURF)
add PM10 data into the package
Main changes in Version 1.0.3 (2016-04-26)
fix VSURF_thres bug in order to always return importance for all variables
(in case of very low sample size, NaN are sometimes produced for importance
of some variables)
add R Journal references in help pages
Main changes in Version 1.0.2 (2015-10-09)
fix in tests: they do not pass on windows 32-bit, but do on all other
platforms.
Main changes in Version 1.0.1 (2015-10-09)
tests were added in the package, testing basic features of
the package.
para parameter of VSURF, VSURF_thres and VSURF_interp is now
called parallel.
add imports to all necessary packages except base
Main changes in Version 1.0.0 (2015-05-15)
WARNING: MAJOR UPDATE.
VSURF is now on github.
Change of name functions :
VSURF.thres becomes VSURF_thres
VSURF.interp becomes VSURF_interp
VSURF.pred becomes VSURF_pred
VSURF.parallel, VSURF.thres.parallel and VSURF.interp.parallel
are removed from the package.
VSURF, VSURF_thres and VSURF_interp can now be used to parallel
executions, by fixing "para = TRUE".
Add a predict method for VSURF objects.
Change of name outputs in VSURF and VSURF_thres :
ord.imp$x becomes imp.mean.dec
ord.imp$ix becomes imp.mean.dec.ind
ord.sd becomes imp.sd.dec
The ntree value now affects all random forests of the procedure
(in all three steps).
S3 methods are no longer exported.
Add several parameters to plot function, allowing to plot
each plot individually from a VSURF object.
Bug fix: in a VSURF run in parallel, there is no error anymore
if the function is called for data with only one variable
Plot functions do not need anymore to have the data on which
the VSURF object was built to be loaded. However, it is still
mandatory if argument var.names is set to TRUE.
Dependencies replaced by Imports.
Main changes in Version 0.8.2 (2014-05-12):
Bug fix: the random seed is now correctly set when using
the VSURF.parallel function with clusterType="FORK"
Bug fix: VSURF function can now handle categorical input
variables. Thanks to ONF researchers for pointing this out.
Main changes in Version 0.8.1 (2014-01-28):
Bug fix: error of the model was wrongly updated in
the VSURF.pred function. Thanks a lot to Dustin Fife.
Main changes in Version 0.8 (2013-11-23):
Parallel version of VSURF added. Three new main functions:
VSURF.parallel, VSURF.thres.parallel and VSURF.interp.parallel.
Default for these functions is to run VSURF in parallel on a
(local) SOCKET cluster with "number of cores detected by R" minus
one core
Addition of a print function for VSURF results
Bug fix: the fact that the prediction step can not run
does not give an error anymore
Main changes in Version 0.7.6 (2013-11-13):
Plot functions changed. It is now possible to plot VI mean
and VI standard deviation against variables names with function
plot.VSURF.thres. By default index variables are plotted, and
var.names argument is added to all plot functions
Bug concerning ylab and yticks fixed
Addition of a warning when using formula method of VSURF,
VSURF.thres, VSURF.interp and VSURF.pred: indices of selected
variables must be reordered to get indices of the original
dataset
Main changes in Version 0.7.5 (2013-10-04):
Only plot functions changed. It is now possible to choose the number
of variables for the VI mean and the VI standard deviation plots.
It is also possible to choose if VI mean and/or VI standard
deviation plots must be plooted by function plot.VSURF.thres
Main changes in Version 0.7 (2013-09-10):
The package can be used with the formula-type call. Hence the package can handle
missing values (NA) (only when used with the formula-type call, as randomForest does)
Update of the plot.VSURF function: the two last graphs show the variables names on the
x-axis
New functions (intermediate plots): plot.VSURF.thres, plot.VSURF.interp, plot.VSURF.pred
Functions renamed: VSURF.interp.tune -> tune.VSURF.interp, VSURF.thres.tune -> tune.thres.tune
and S3method are now used for these functions
Main changes in Version 0.6 (2013-07-23):
New functions: plot.VSURF, summary.VSURF, VSURF.interp.tune, VSURF.thres.tune.
Addition of a dataset: toys
Addition of new outputs of existing functions.
Bug fix: min.thres component of VSURF results list returns now the threshold value.