R: Method for 'glm' that tests for data separation and finds...

detect_separation {detectseparation}

R Documentation

Method for `glm` that tests for data separation and finds which parameters have infinite maximum likelihood estimates in generalized linear models with binomial responses

Description

detect_separation is a method for glm that tests for the occurrence of complete or quasi-complete separation in datasets for binomial response generalized linear models, and finds which of the parameters will have infinite maximum likelihood estimates. detect_separation relies on the linear programming methods developed in Konis (2007).

Usage

detect_separation(
  x,
  y,
  weights = rep(1, nobs),
  start = NULL,
  etastart = NULL,
  mustart = NULL,
  offset = rep(0, nobs),
  family = gaussian(),
  control = list(),
  intercept = TRUE,
  singular.ok = TRUE
)

detectSeparation(
  x,
  y,
  weights = rep(1, nobs),
  start = NULL,
  etastart = NULL,
  mustart = NULL,
  offset = rep(0, nobs),
  family = gaussian(),
  control = list(),
  intercept = TRUE,
  singular.ok = TRUE
)

Arguments

`x`	`x` is a design matrix of dimension `n * p`.
`y`	`y` is a vector of observations of length `n`.
`weights`	an optional vector of ‘prior weights’ to be used in the fitting process. Should be `NULL` or a numeric vector.
`start`	currently not used.
`etastart`	currently not used.
`mustart`	currently not used.
`offset`	this can be used to specify an a priori known component to be included in the linear predictor during fitting. This should be `NULL` or a numeric vector of length equal to the number of cases. One or more `offset` terms can be included in the formula instead or as well, and if more than one is specified their sum is used. See `model.offset`.
`family`	a description of the error distribution and link function to be used in the model. For `glm` this can be a character string naming a family function, a family function or the result of a call to a family function. For `glm.fit` only the third option is supported. (See `family` for details of family functions.)
`control`	a list of parameters controlling separation detection. See `detect_separation_control` for details.
`intercept`	logical. Should an intercept be included in the null model?
`singular.ok`	logical. If `FALSE`, a singular model is an error.

Details

detect_separation is a wrapper to the separator_ROI function and separator_lpSolveAPI function (a modified version of the separator function from the **safeBinaryRegression** R package). detect_separation can be passed directly as a method to the glm function. See, examples.

The coefficients method extracts a vector of values for each of the model parameters under the following convention: 0 if the maximum likelihood estimate of the parameter is finite, and Inf or -Inf if the maximum likelihood estimate of the parameter if plus or minus infinity. This convention makes it easy to adjust the maximum likelihood estimates to their actual values by element-wise addition.

detectSeparation is an alias for detect_separation.

Value

A list that inherits from class detect_separation, glm and lm. A print method is provided for detect_separation objects.

Note

For the definition of complete and quasi-complete separation, see Albert and Anderson (1984). Kosmidis and Firth (2021) prove that the reduced-bias estimator that results by the penalization of the logistic regression log-likelihood by Jeffreys prior takes always finite values, even when some of the maximum likelihood estimates are infinite. The reduced-bias estimates can be computed using the brglm2 R package.

detect_separation was designed in 2017 by Ioannis Kosmidis for the **brglm2** R package, after correspondence with Kjell Konis, and a port of the separator function had been included in **brglm2** under the permission of Kjell Konis.

In 2020, detect_separation and check_infinite_estimates were moved outside **brglm2** into the dedicated **detectseparation** package. Dirk Schumacher authored the separator_ROI function, which depends on the **ROI** R package and is now the default implementation used for detecting separation.

Author(s)

Ioannis Kosmidis [aut, cre] ioannis.kosmidis@warwick.ac.uk, Dirk Schumacher [aut] mail@dirk-schumacher.net, Kjell Konis [ctb] kjell.konis@me.com

References

Konis K. (2007). *Linear Programming Algorithms for Detecting Separated Data in Binary Logistic Regression Models*. DPhil. University of Oxford. https://ora.ox.ac.uk/objects/uuid:8f9ee0d0-d78e-4101-9ab4-f9cbceed2a2a

Konis K. (2013). safeBinaryRegression: Safe Binary Regression. R package version 0.1-3. https://CRAN.R-project.org/package=safeBinaryRegression

Kosmidis I. and Firth D. (2021). Jeffreys-prior penalty, finiteness and shrinkage in binomial-response generalized linear models. *Biometrika*, **108**, 71–82

Examples


## endometrial data from Heinze \& Schemper (2002) (see ?endometrial)
data("endometrial", package = "detectseparation")
endometrial_sep <- glm(HG ~ NV + PI + EH, data = endometrial,
                       family = binomial("logit"),
                       method = "detect_separation")
endometrial_sep
## The maximum likelihood estimate for NV is infinite
summary(update(endometrial_sep, method = "glm.fit"))


## Example inspired by unpublished microeconometrics lecture notes by
## Achim Zeileis https://eeecon.uibk.ac.at/~zeileis/
## The maximum likelihood estimate of sourhernyes is infinite
if (requireNamespace("AER", quietly = TRUE)) {
    data("MurderRates", package = "AER")
    murder_sep <- glm(I(executions > 0) ~ time + income +
                      noncauc + lfp + southern, data = MurderRates,
                      family = binomial(), method = "detect_separation")
    murder_sep
    ## which is also evident by the large estimated standard error for NV
    murder_glm <- update(murder_sep, method = "glm.fit")
    summary(murder_glm)
    ## and is also reveal by the divergence of the NV column of the
    ## result from the more computationally intensive check
    plot(check_infinite_estimates(murder_glm))
    ## Mean bias reduction via adjusted scores results in finite estimates
    if (requireNamespace("brglm2", quietly = TRUE))
        update(murder_glm, method = brglm2::brglm_fit)
}

[Package detectseparation version 0.2 Index]

Method for glm that tests for data separation and finds which parameters have infinite maximum likelihood estimates in generalized linear models with binomial responses