perturb: Perturbation analysis to evaluate collinearity

In perturb: Tools for Evaluating Collinearity

Description

Adds random noise to selected variables to evaluate collinearity. Also suitable for other models than linear regression and for categorical independent variables

Usage

perturb(mod, pvars = NULL, prange = NULL, ptrans = NULL,
pfac = NULL, uniform = FALSE, niter = 100)

## S3 method for class 'perturb'
summary(object,dec.places=3,full=FALSE,...)

## S3 method for class 'perturb'
print.summary(x,...)

Arguments

mod	A model object, not necessarily type lm
pvars	Contains an array of variables to be perturbed. Random values are added to the variable, after which the model is re-estimated.
prange	Contains an array of values determining the magnitude of perturbations. There should be as many prange values as pvars variables.
ptrans	Contains an array of transformations to be applied. Each element should contain valid R syntax in quotes for deriving one of the pvars as a function of other variables.
pfac	Contains a list of categorical variables to be perturbed and parameters controlling the reclassification process. The first component must be a factor name. The name for the first component is ignored. Other list components should correspond with options for reclassify. The usage of these parameters is discussed more fully below under the heading “Categorical variables”.
uniform	If uniform=TRUE, random values from a uniform distribution unif(-\emph{x}/2,\emph{x}/2) are added to the perturb variables, where x is the prange value corresponding with each pvars variable. The default is to add values from a normal distribution N(0,x).
niter	Indicates the number of times to re-estimate the model. Default is 100.
object	a perturb object to be summarized
x	a summary.perturb object to be printed
dec.places	number of decimal places to use when printing
full	if TRUE, some extra information is printed
...	arguments to be passed on to or from other methods. Print options for class matrix may be used, e.g. print.gap

Details

Perturb is a tool for assessing the impact of small random changes (perturbations) to variables on parameter estimates. It is an alternative for collinearity diagnostics such as vif in the car package, vif in the rms package or colldiag in this package. Perturb is particularly useful for evaluating collinearity if interactions are present or nonlinear transformations of variables, e.g. a squared term. Perturb can show how the perturbations affect the estimates of a variable and terms derived from it whereas other collinearity diagnostics simply treat interactions and transformations as regular independent variables. Perturb is not limited to linear regression but can be used for all regression-like models. Perturb can also deal with categorical variables by randomly misclassifying them to assess the impact on parameter estimates.

Perturb works by adding a small random “perturbation” value to selected independent variables, then re-estimating the model. This process is repeated niter times, after which a summary of the means, standard deviation, minimum and maximum of the parameter estimates is displayed. If collinearity is a serious problem in the data, then the estimates will be unstable and vary strongly.

Perturb can be used with categorical variables. Categorical variables are reclassified according to a table of reclassification probabilities. Random numbers determine to which category each case is reclassified at each iteration. The reclassification probabilities are specified to make reclassification to the same category highly likely. For ordered variables, short distance reclassification can be made more likely than long distance. See the section on “Categorical variables” and reclassify for further details.

Value

An object of class “perturb”. The main result is contained in coef.table, which contains the parameter estimates for each iteration of the perturbation analysis. summary prints the mean, standard deviation, minimum and maximum of coef.table over the iterations. If the option full is specified, reclassify prints additional information on how the reclassification probabilities were derived. Summary also prints information on the transformed model formula.

coef.table	Estimated coefficients for each iteration of the perturbation analysis
formula	The model formula used
pvars	The continuous variables perturbed in the analysis
prange	Magnitude of the perturbations
ptrans2	The transformations using the temporary variables of the perturbation analysis
reclassify.tables	objects produced by reclassify for each factor in the perturbation analysis
formula2	The model formula using temporary variables
distribution	“normal” or “uniform”, the distribution from which to draw random numbers

Categorical variables

In a perturbation analysis, categorical variables are reclassified with a high probability of remaining in the same category. This could be accomplished in several ways. reclassify lets you specify the target percentage reclassification, then adjusts the reclassification frequencies so that the expected frequencies of the reclassified variable are the same as those of the original. In addition, reclassify imposes a meaningful pattern of association between the original and the reclassified variable. See reclassify for details.

Categorical variables are specified in perturb as a list in the pfac option. The first (unnamed) component is the factor to be reclassified. The names of following components should be valid reclassify options follows by appropriate values. For example, to reclassify the factor “type” with a 95% probability of reclassify to the same category, use:

p2<-perturb(m2,pvars=c("income","education"),prange=c(1,1),
pfac=list("type",pcnt=95))

This command will iteratively re-estimate model m2 100 times (default). Random values from a normal distribution with a standard deviation of 1 will be added to the variables income and education. Reclassify creates a table of initial reclassification probabilities for type with a 95% probability of reclassification to the same category. This initial table is adjusted and the final reclassification probabilities printed in the output are subsequently used to reclassify type at each iteration.

Use a list of lists to specify a model with more than one reclassification factor, for example:

pfac=list(list("fegp6",pcnt=95),list("eyrc",pcnt=m1),list("expc",pcnt=m2))
q<-perturb(r1,pfac=pfac)

Note

Perturb can be used with estimation procedures other than lm. On the other hand, collinearity is a result of extreme (multiple) correlation among independent variables. Another option is vif in the rms package vif in the car package, or colldiag, which use only the independent variables of a regression model. This will usually be a faster solution since maximum likelihood procedures require iterative estimation for each iteration of the perturbation analysis. It is possible though that certain procedures are more sensitive to collinearity than lm, in which case perturb could be a better solution.

Author(s)

John Hendrickx [e-mail]

References

D. Belsley, E. Kuh, and R. Welsch (1980). Regression Diagnostics. Wiley.

Belsley, D.A. (1991). Conditioning diagnostics, collinearity and weak data in regression. New York: John Wiley & Sons.

Hendrickx, John, Ben Pelzer. (2004). Collinearity involving ordered and unordered categorical variables. Paper presented at the RC33 conference in Amsterdam, August 17-20 2004. Available at https://www.researchgate.net/publication/235994590_Collinearity_involving_ordered_and_unordered_categorical_variables

See Also

reclassify, colldiag, [car]vif, [rms]vif

Examples

library(car)
data(Duncan)
attach(Duncan)
m1<-lm(prestige~income+education)
summary(m1)
anova(m1)
vif(m1)
p1<-perturb(m1,pvars=c("income","education"),prange=c(1,1))
summary(p1)
m2<-lm(prestige~income+education+type)
summary(m2)
anova(m2)
vif(m2)
p2<-perturb(m2,pvars=c("income","education"),prange=c(1,1),pfac=list("type",pcnt=95))
summary(p2)

## Not run: 
r1<-lm(ses~fegp6+educyr+eyr+exp2)
summary(r1)
q<-perturb(r1,c("eyr","exp"),c(2.5,2.5),ptrans="exp2<-exp^2")
summary(q)

fegp6<-as.factor(fegp6)

# eyr and exp also as factors
eyrc<-cut(eyr,c(min(eyr),40,50,60,70,80,max(eyr)),include.lowest=T,right=F)
table(eyrc)
expc<-cut(exp,c(0,10,20,max(exp)),include.lowest=T,right=F)
table(expc)

# rough initial reclassification probabilities,
# program will ensure they sum to 100 row-wise
m1<-matrix(0,nlevels(eyrc),nlevels(eyrc))
m1[row(m1)==col(m1)]<-80
m1[abs(row(m1)-col(m1))==1]<-8
m1[abs(row(m1)-col(m1))==2]<-2
m1

m2<-matrix(0,nlevels(expc),nlevels(expc))
m2[row(m2)==col(m2)]<-80
m2[abs(row(m2)-col(m2))==1]<-10
m2[abs(row(m2)-col(m2))==2]<-2
m2

r2<-lm(ses~fegp6+eyrc+expc)
summary(r2)
pfac=list(list("fegp6",pcnt=95),list("eyrc",pcnt=m1),list("expc",pcnt=m2))
q2<-perturb(r2,pfac=pfac,niter=1)
summary(q2)

## End(Not run)

perturb documentation built on May 2, 2019, 3:24 a.m.