np.conmode: Kernel Modal Regression with Mixed Data Types

In np: Nonparametric Kernel Smoothing Methods for Mixed Data Types

Kernel Modal Regression with Mixed Data Types

Description

npconmode performs kernel modal regression on mixed data, and finds the conditional mode given a set of training data, consisting of explanatory data and dependent data, and possibly evaluation data. Automatically computes various in sample and out of sample measures of accuracy.

Usage

npconmode(bws, 
          ...)

## S3 method for class 'formula'
npconmode(bws, 
          data = NULL,
          newdata = NULL, 
          ...)

## Default S3 method:
npconmode(bws, 
          txdat, 
          tydat, 
          nomad = FALSE,
          proper = NULL,
          proper.control = list(),
          probabilities = FALSE,
          gradients = FALSE,
          level = NULL,
          ...)

## S3 method for class 'conbandwidth'
npconmode(bws,
          txdat = stop("invoked without training data 'txdat'"),
          tydat = stop("invoked without training data 'tydat'"),
          exdat,
          eydat,
          proper = NULL,
          proper.control = list(),
          probabilities = FALSE,
          gradients = FALSE,
          level = NULL,
          ...)

## S3 method for class 'conmode'
predict(object,
          newdata = NULL,
          type = c("class", "prob"),
          se.fit = FALSE,
          ...)

## S3 method for class 'conmode'
plot(x, ...)

Arguments

Data, Bandwidth Inputs And Formula Interface

These arguments identify the bandwidth specification, formula/data interface, and training data.

bws	a bandwidth specification. This can be set as a conbandwidth object returned from an invocation of npcdensbw
data	an optional data frame, list or environment (or object coercible to a data frame by as.data.frame) containing the variables in the model. If not found in data, the variables are taken from environment(bws), typically the environment from which npcdensbw was called.
txdat	a p-variate data frame of explanatory data (conditioning data) used to calculate the regression estimators. Defaults to the training data used to compute the bandwidth object.
tydat	a one (1) dimensional vector of unordered or ordered factors, containing the dependent data. Defaults to the training data used to compute the bandwidth object.
object	an object of class "conmode" returned by npconmode.
x	an object of class "conmode" returned by npconmode.

Evaluation Data

These arguments control where the conditional mode is evaluated.

exdat	a p-variate data frame of points on which the regression will be estimated (evaluation data). By default, evaluation takes place on the data provided by txdat.
eydat	a one (1) dimensional numeric or integer vector of the true values (outcomes) of the dependent variable. By default, evaluation takes place on the data provided by tydat.
newdata	An optional data frame in which to look for evaluation data. If omitted, the training data are used.
type	prediction type for predict.conmode. Use "class" to return modal class predictions and "prob" to return the full class-probability matrix. Probability prediction requires either a stored probability matrix or an evaluation path with probabilities=TRUE.
se.fit	a logical value for predict.conmode. If TRUE and type="prob", return a list with components fit and se.fit, containing the class-probability matrix and matching asymptotic standard-error matrix. Standard errors are for the smooth class-probability target, not for the discrete modal class label.

Probability And Gradient Controls

These arguments control stored class probabilities, proper probability normalization, and level-specific class-probability effects.

probabilities	a logical value. If TRUE, store the full matrix of fitted probabilities over the discrete response support in the returned object. The default FALSE keeps returned objects compact. If gradients=TRUE, probabilities are stored automatically because they are the object-fed target for plot.conmode.
gradients	a logical value. If TRUE, compute and store class-probability gradients/effects for one response level with respect to the conditioning variables. These are derivatives for continuous conditioning variables and the corresponding smooth finite-change effects for discrete conditioning variables as produced by the underlying npcdens gradient route. The target is the smooth class probability \Pr(Y=\ell\mid X=x), not the derivative of the discrete modal class label.
level	response level for class-probability gradients/effects and plot.conmode class-probability displays. If omitted, the default is the base/reference response level, levels(y)[1], for both factor and ordered responses. Users should supply level explicitly when a particular binary or multinomial outcome probability is of substantive interest.
proper	a logical value or NULL. If TRUE, fitted probabilities over the discrete response support are projected onto the probability simplex before modal selection. If FALSE, legacy raw per-level values are used. If NULL, the default is estimator-aware: FALSE for regtype="lc" and TRUE otherwise.
proper.control	a list of controls for discrete probability properization. Currently tol may be supplied to set the numerical tolerance for non-negativity and unit-mass checks.

Local-Polynomial Degree And Bandwidth Search

This argument controls the recommended automatic local-polynomial NOMAD route, which jointly selects continuous polynomial degree and bandwidths when conditional-density bandwidths are computed inside npconmode.

nomad

logical shortcut passed through to npcdensbw when bandwidths are computed inside npconmode. When TRUE, the conditional-density bandwidth route fills any missing values among regtype, search.engine, degree.select, bernstein.basis, degree.min, degree.max, degree.verify, and bwtype with the recommended automatic local-polynomial degree-and-bandwidth NOMAD preset documented in npcdensbw. Additional NOMAD tuning arguments such as nomad.nmulti may also be supplied through ...; nmulti remains the outer restart count while nomad.nmulti controls inner crs::snomadr() multistarts within each outer restart. Automatic NOMAD degree search requires at least one continuous explanatory variable. After fitting, inspect fit$bws$nomad.shortcut on the returned object fit to see the normalized shortcut metadata.

Additional Arguments

Further arguments are passed to the bandwidth-selection counterpart, prediction/evaluation route, or plot route as appropriate.

...

additional arguments supplied to npcdensbw when bandwidths are computed internally, or arguments needed to interpret a numeric bws vector. This is where bandwidth-selection controls such as bwmethod, bwtype, and bwscaling, kernel/support controls such as cxkertype, cykertype, cxkerorder, cykerorder, cxkerbound, and cykerbound, categorical kernel controls such as uxkertype, uykertype, oxkertype, and oykertype, search controls such as nmulti and scale.factor.search.lower, and local-polynomial/NOMAD controls such as regtype, degree, bernstein.basis, degree.select, and nomad.nmulti are supplied. In predict.conmode, additional arguments are passed to npconmode for evaluation with the stored bandwidth object; native exdat and eydat take precedence over newdata. In plot.conmode, additional arguments control the object-fed probability/effect display; common controls include gradients, level, output, data_rug, layout, legend, view, neval, grid_control, perspective, plot.vars, renderer, and graphics arguments. The default view="sample" draws the stored fitted probabilities/effects at the fitted evaluation points. The view="fixed" route constructs one-dimensional object-fed slices over each conditioning variable, holding the remaining variables at their uocquantile median/mode values; np_grid_control(xtrim=..., xq=...) may be used to adjust the slice range and holdout quantiles. With perspective=TRUE, the same fixed-grid route draws a base-graphics probability surface for one selected response level over two continuous conditioning variables; use plot.vars to name the displayed pair when more than two continuous conditioning variables are present; renderer="rgl" requests the corresponding interactive surface when rgl is available. The public output="both" spelling is accepted as an alias for the historical output="plot-data" behavior. For class-probability plots, errors="asymptotic" adds probability-level asymptotic standard errors and intervals for the selected response level. These intervals target the smooth probability \Pr(Y=\ell\mid X=x), not the discrete modal class label. Rows whose probabilities were materially repaired by simplex projection report NA standard errors rather than treating raw conditional-density standard errors as projected-probability standard errors. Bootstrap intervals are available for one-dimensional view="sample" and view="fixed" probability plots and use the stored bandwidth object without recomputing bandwidths. Surface asymptotic intervals are available as output="data" payload columns; surface band rendering and surface bootstrap intervals are intentionally deferred. See npcdensbw and plot.np for the complete bandwidth-selection and plotting argument surfaces.

Details

Documentation guide: see np.kernels for kernels, np.options for global options, and plot for plotting options.

If bws is not an explicit conbandwidth object, npconmode computes conditional density bandwidths by forwarding the call to npcdensbw. The resulting conbandwidth object is stored unchanged in the returned object's bws component. Regression type, local-polynomial degree, and NOMAD/search metadata are also mirrored on the returned conmode object for convenient inspection and summary reporting; the bandwidth object remains the canonical source.

For non-local-constant conditional-mode fits, npconmode constructs the full set of fitted probabilities over the discrete response support and projects them onto the probability simplex before selecting and reporting the modal outcome. Thus the probabilities used for modal selection are non-negative and sum to one over the discrete support. For binary outcomes this is the complement contract \Pr(Y=\ell_2\mid X=x)=1-\Pr(Y=\ell_1\mid X=x). Local-constant fits are already proper by construction, so omitted proper resolves to FALSE for regtype="lc" and to TRUE otherwise.

The predict method follows the usual S3 newdata convention. With no evaluation arguments, predict(fit) extracts the stored modal class and predict(fit, type="prob") extracts stored class probabilities when the object was fitted with probabilities=TRUE. With newdata, predict evaluates the conditional mode at the supplied rows using the stored bandwidth object. Use type="prob" to return the full matrix of fitted class probabilities at the evaluation rows. Use se.fit=TRUE with type="prob" to return a list containing the class-probability matrix and the matching asymptotic standard-error matrix. Native evaluator arguments exdat and eydat remain available for advanced workflows and take precedence if supplied.

Value

npconmode returns a conmode object with the following components:

bws	the conbandwidth object used to compute the conditional mode
conmode	a vector of type factor (or ordered factor) containing the conditional mode at each evaluation point
condens	a vector of numeric type containing the modal density estimates at each evaluation point
conderr	a vector of numeric type containing asymptotic standard errors for the modal density estimates at each evaluation point. If a row is materially properized by probability projection, this value is set to NA for that row rather than reporting a standard error for the unrepaired raw probability.
xeval	a data frame of evaluation points
yeval	a vector of type factor (or ordered factor) containing the actual outcomes, or NA if not provided
confusion.matrix	the confusion matrix or NA if outcomes are not available
CCR.overall	the overall correct classification ratio, or NA if outcomes are not available
CCR.byoutcome	a numeric vector containing the correct classification ratio by outcome, or NA if outcomes are not available
fit.mcfadden	the McFadden-Puig-Kerschner performance measure or NA if outcomes are not available
probabilities	if requested, a matrix of fitted probabilities over the discrete response support
probability.levels	if probabilities are stored, the response support corresponding to the probability matrix columns
probability.errors	if probabilities are stored, a matrix of asymptotic standard errors for the raw selected-level conditional probability estimates, with rows set to NA where simplex projection materially repaired the fitted probability vector
probability.repaired.rows	if probabilities are stored, a logical vector identifying rows whose fitted probability vector was materially repaired by proper probability projection
probability.gradients	if gradients=TRUE, a matrix whose entries are class-probability gradients/effects for one selected response level, indexed by evaluation row and conditioning variable
probability.gradient.level, probability.gradient.names, probability.gradient.info	metadata describing the response support, conditioning variables, and interpretation of probability.gradients
proper.requested, proper.applied, proper.info	metadata describing whether discrete probability properization was requested, whether any row was materially projected, and diagnostics for non-negativity and unit-mass checks
regtype, degree, nomad, search.engine	metadata mirrored from bws describing the conditional density regression type, local-polynomial degree, whether NOMAD automatic degree search was used, and the search engine when available
degree.search, nomad.shortcut, nomad.time, powell.time	detailed search metadata mirrored from bws when automatic degree search or NOMAD/Powell refinement was used

The function predict may be used to extract conditional mode class predictions, while fitted extracts the conditional density estimates at the conditional mode from the resulting object. The function gradients extracts class-probability gradients/effects when gradients=TRUE. Also, summary and plot support conmode objects. For plot.conmode, first fit with probabilities=TRUE so the plot can remain object-fed. The default plot displays the fitted probability for the base/reference response level levels(y)[1]; use plot(fit, level=...) to select another outcome and plot(fit, gradients=TRUE) to display stored class-probability effects. The default view="sample" draws stored object-fed probability/effect payloads at the fitted evaluation points. Use view="fixed" and neval to draw object-fed one-dimensional slices over each conditioning variable, with other variables held at their median/mode values. Use perspective=TRUE to draw a base-graphics probability surface for one selected response level over two continuous conditioning variables, and renderer="rgl" for the corresponding interactive surface. Use errors="asymptotic" for probability-level standard errors and intervals in one-dimensional plots, or with output="data" for surface interval payloads. Bootstrap intervals and surface band rendering are not yet implemented for plot.conmode.

Book And Method Pointers

The conditional-mode target is \arg\max_y \Pr(Y=y\mid X=x) for a discrete response. In practice npconmode estimates the conditional probability of each response support point using npcdensbw / npcdens, optionally projects non-local-constant fitted probabilities onto the probability simplex, and then reports the modal support point.

Setting gradients=TRUE stores class-probability effects for one response level. If level is omitted, the base/reference response level levels(y)[1] is used. These effects are useful for asking how the fitted probability of a selected class changes with each covariate; they are not gradients of the arg max classification rule itself.

For book-length background, see Racine (2019), Chapter 4 Conditional Probability Density and Cumulative Distribution Functions, especially the binary and multinomial choice material, and Li and Racine (2007), Chapter 5 Conditional Density Estimation together with Chapter 4 Kernel Estimation with Mixed Data.

Usage Issues

If you are using data of mixed types, then it is advisable to use the data.frame function to construct your input data and not cbind, since cbind will typically not work as intended on mixed data types and will coerce the data to the same type.

Author(s)

Tristen Hayfield [e-mail], Jeffrey S. Racine [e-mail]

References

Aitchison, J. and C.G.G. Aitken (1976), “Multivariate binary discrimination by the kernel method,” Biometrika, 63, 413-420.

Hall, P. and J.S. Racine and Q. Li (2004), “Cross-validation and the estimation of conditional probability densities,” Journal of the American Statistical Association, 99, 1015-1026.

Li, Q. and J.S. Racine (2007), Nonparametric Econometrics: Theory and Practice, Princeton University Press.

McFadden, D. and C. Puig and D. Kerschner (1977), “Determinants of the long-run demand for electricity,” Proceedings of the American Statistical Association (Business and Economics Section), 109-117.

Pagan, A. and A. Ullah (1999), Nonparametric Econometrics, Cambridge University Press.

Scott, D.W. (1992), Multivariate Density Estimation. Theory, Practice and Visualization, New York: Wiley.

Silverman, B.W. (1986), Density Estimation, London: Chapman and Hall.

Wang, M.C. and J. van Ryzin (1981), “A class of smooth estimators for discrete distributions,” Biometrika, 68, 301-309.

See Also

np.kernels, np.options, plot, npcdensbw.

Examples

## Not run: 
# EXAMPLE 1 (INTERFACE=FORMULA): For this example, we use the
# birthweight data taken from the MASS library, and compute a parametric
# logit model and a nonparametric conditional mode model. We then
# compare their confusion matrices and summary measures of
# classification ability.

library("MASS")
data("birthwt")

birthwt$low <- factor(birthwt$low)
birthwt$smoke <- factor(birthwt$smoke)
birthwt$race <- factor(birthwt$race)
birthwt$ht <- factor(birthwt$ht)
birthwt$ui <- factor(birthwt$ui)
birthwt$ftv <- ordered(birthwt$ftv)

with(birthwt, {

# Fit a parametric logit model with low (0/1) as the dependent
# variable and age, lwt, and smoke (0/1) as the covariates

# From ?birthwt
# 'low' indicator of birth weight less than 2.5kg
# 'smoke' smoking status during pregnancy
# 'race' mother's race ('1' = white, '2' = black, '3' = other)
# 'ht' history of hypertension
# 'ui' presence of uterine irritability
# 'ftv' number of physician visits during the first trimester
# 'age' mother's age in years
# 'lwt' mother's weight in pounds at last menstrual period

model.logit <- glm(low~smoke+
                   race+
                   ht+
                   ui+
                   ftv+
                   age+
                   lwt,
                   family=binomial(link=logit))

# Generate the confusion matrix and correct classification ratio

cm <- table(low, ifelse(fitted(model.logit)>0.5, 1, 0))
ccr <- sum(diag(cm))/sum(cm)

# Now do the same with a nonparametric model.  Note - this may take a
# few minutes depending on the speed of your computer...

bw <- npcdensbw(formula=low~smoke+
                race+
                ht+
                ui+
                ftv+
                age+
                lwt,
                data=birthwt)

model.np <- npconmode(bws=bw)

# Compare confusion matrices from the logit and nonparametric model

# Logit

cm
ccr

# Nonparametric
summary(model.np)

# Predict modal classes and fitted class probabilities at selected rows
new.birthwt <- birthwt[1:5, c("smoke", "race", "ht", "ui", "ftv", "age", "lwt")]
predict(model.np, newdata=new.birthwt)
predict(npconmode(bws=bw, probabilities=TRUE),
        newdata=new.birthwt, type="prob")

})

# EXAMPLE 1 (INTERFACE=DATA FRAME): For this example, we use the
# birthweight data taken from the MASS library, and compute a parametric
# logit model and a nonparametric conditional mode model. We then
# compare their confusion matrices and summary measures of
# classification ability.

library("MASS")
data("birthwt")
with(birthwt, {

# Fit a parametric logit model with low (0/1) as the dependent
# variable and age, lwt, and smoke (0/1) as the covariates

# From ?birthwt
# 'low' indicator of birth weight less than 2.5kg
# 'smoke' smoking status during pregnancy
# 'race' mother's race ('1' = white, '2' = black, '3' = other)
# 'ht' history of hypertension
# 'ui' presence of uterine irritability
# 'ftv' number of physician visits during the first trimester
# 'age' mother's age in years
# 'lwt' mother's weight in pounds at last menstrual period

model.logit <- glm(low~factor(smoke)+
                   factor(race)+
                   factor(ht)+
                   factor(ui)+
                   ordered(ftv)+
                   age+
                   lwt,
                   family=binomial(link=logit))

# Generate the confusion matrix and correct classification ratio

cm <- table(low, ifelse(fitted(model.logit)>0.5, 1, 0))
ccr <- sum(diag(cm))/sum(cm)

# Now do the same with a nonparametric model...

X <- data.frame(factor(smoke),
                factor(race),
                factor(ht),
                factor(ui),
                ordered(ftv),
                age,
                lwt)

y <- factor(low)

# Note - this may take a few minutes depending on the speed of your
# computer...

bw <- npcdensbw(xdat=X, ydat=y)

model.np <- npconmode(bws=bw)

# Compare confusion matrices from the logit and nonparametric model

# Logit

cm
ccr

# Nonparametric
summary(model.np)

})

# EXAMPLE 3 (CLASS PROBABILITY EFFECTS): compute and plot
# class-probability gradients/effects for one selected response level.
# This example uses a small artificial sample so that it runs quickly.

set.seed(42)
n <- 100
x <- seq(-1, 1, length.out=n)
y <- factor(rbinom(n, 1, plogis(1.5*x)), levels=0:1)

model.effects <- npconmode(y~x,
                           regtype="ll",
                           bwmethod="cv.ls",
                           nmulti=1,
                           probabilities=TRUE,
                           gradients=TRUE)

gradients(model.effects)
plot(model.effects)
plot(model.effects, view="fixed", neval=25)
plot(model.effects, gradients=TRUE)
plot(model.effects, gradients=TRUE, view="fixed", neval=25)

## A two-continuous-predictor fit can be displayed as a probability surface.
## The default level is the base/reference response level.

z <- runif(n, -1, 1)
y2 <- factor(rbinom(n, 1, plogis(1.5*x - z)), levels=0:1)
model.surface <- npconmode(y2~x+z,
                           regtype="ll",
                           bwmethod="cv.ls",
                           nmulti=1,
                           probabilities=TRUE)
plot(model.surface, perspective=TRUE, neval=15)

## End(Not run) 

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