R/marginalModelPlot.R

Defines functions mmps marginalModelPlots mmp marginalModelPlot

Documented in marginalModelPlot marginalModelPlots mmp mmps

#############################################
# marginal model plots    Rev 12/30/09
# 15 March 2010 changed to make
#   mmps(lm(longley)) work without specifying data or response
#   fixed bug  when only one plot is requested --- suppress call to par()
#   added 'outerLegend' to label lines
#   modified to work correctly with
# 28 May 2010 S. Weisberg, fixed bugs in logistic models
#   changed line thickness of mean smooths
#   excluded SD smooth from bernoulli models
#   added grid lines
# 15 August 2010 fixed colors of points to work properly
# 16 January 2011 improved handling of splines and polynomials in mmps to
#    allow plots against base variables (e.g., bs(x, 3) could be
#    replaced by just x in the 'terms' argument to mmps.
# 16 June 2011 allow layout=NA, in which case the layout is not set in this
#  function, so it is the responsibility of the user
# 14 September 2012 improved the smoothers
# 22 September 2012 added conditioning on one categorical regressor
# 2017-02-13: consolidated smooth and id arguments. J. Fox
# 2017-10-29: Changed line type of smooth of the data to 1 as advertised
# 2017-10-29: Changed default color palette from palette() to carPalette()
# 2019-05-17: in mmp.glm, default horizontal variable when fitted=TRUE is now the
#             fitted values for lm and the linear predictor for glm
# 2019-05-17: added ylab arg to mmp() methods. J. Fox
# 2019-11-14: change class(x) == "y" to inherits(x, "y")
#############################################

marginalModelPlot <- function(...){
    mmp(...)
}

mmp <- function(model, ...){
    UseMethod("mmp")
}

mmp.lm <- function (model, variable, sd = FALSE,
                    xlab = deparse(substitute(variable)),
                    smooth=TRUE, key=TRUE, pch, groups=NULL, ...){
    smooth <- applyDefaults(smooth, defaults=list(smoother=loessLine, span=2/3), type="smooth")
    mmp.default(model, variable, sd, xlab, smooth=smooth, key, pch=pch, groups=groups, ...)
}

mmp.default <- function (model, variable, sd = FALSE,
                         xlab = deparse(substitute(variable)), ylab, smooth=TRUE, key=TRUE, pch, groups=NULL,
                         col.line = carPalette()[c(2, 8)], col=carPalette()[1],
                         id=FALSE, grid=TRUE, ...){
    id <- applyDefaults(id, defaults=list(method="y", n=2, cex=1, col=carPalette()[1], location="lr"), type="id")
    if (isFALSE(id)){
        id.n <- 0
        id.method <- "none"
        labels <- id.cex <- id.col <- id.location <- NULL
    }
    else{
        labels <- id$labels
        if (is.null(labels)) labels <- names((residuals(model)))
        id.method <- id$method
        id.n <- if ("identify" %in% id.method) Inf else id$n
        id.cex <- id$cex
        id.col <- id$col
        id.location <- id$location
    }
    smoother.args <- applyDefaults(smooth, defaults=list(smoother=loessLine, span=2/3), type="smooth")
    if (!isFALSE(smoother.args)) {
        smoother <- smoother.args$smoother
        smoother.args$smoother <- NULL
    }
    else smoother <- "none"
    lwd <- match.call(expand.dots=TRUE)$lwd
    if(missing(pch)) pch <- 1
    groups.col <- col
    if (!is.null(groups)){
        if(is.data.frame(groups)) {
            groups.label <- colnames(groups)[1]
            groups <- groups[,1]
        } else {
            groups.label <- deparse(substitute(groups))
        }
        groups.levels <- unique(na.omit(groups))
        for (j in 1:(length(groups.levels))) {
            pch[groups==groups.levels[j]] <- j
            groups.col[groups==groups.levels[j]] <- carPalette()[j]}
    }
    if  (!is.null(attr(model$model, "na.action"))) {
        if (attr(attr(model$model, "na.action"), "class") == "exclude")
            model <- update(model, na.action=na.omit)}
    if (missing(variable)) {
        xlab <- "Fitted values"
        u <- fitted(model)
    } else {
        u <- variable}
    resp <- model.response(model.frame(model))
    if (missing(ylab)) ylab <- colnames(model$model[1])
    plot(u, resp,
         xlab = xlab, ylab = ylab, type="n", ...)
    if(grid){
        grid(lty=1, equilogs=FALSE)
        box()}
    points(u, model$model[ , 1], col=groups.col, pch=pch, ...)
    if (!(is.character(smoother) && smoother == "none")){
        ow <- options(warn=-1)
        on.exit(options(ow))
        smoother.args$lty.spread <- 1
        smoother.args$lwd <- smoother.args$lwd.spread <- if(is.null(lwd)) 2 else lwd
        if(is.null(groups)) {
            smoother.args$lty.smooth <- 1
            smoother(u, resp, col.line[1], log.x=FALSE, log.y=FALSE, spread=sd,
                     smoother.args=smoother.args)
            smoother.args$lty.smooth <- smoother.args$lty.spread <- 2
            # 11/21/14:  SD smooth under the model corrected by adding the 'offset'
            smoother(u, predict(model), col.line[2], log.x=FALSE, log.y=FALSE, spread=sd,
                     smoother.args=smoother.args, offset=sigmaHat(model))
            #          smoother.args=smoother.args)
            if(key){
                outerLegend(c("Data", "Model"), lty=1:2, col=col.line,
                            bty="n", cex=0.75, fill=col.line, border=col.line, horiz=TRUE,
                            offset=0)
            }
        } else {
            for (j in 1:length(groups.levels)) {
                smoother.args$lwd <- if(is.null(lwd)) 1.75 else lwd
                smoother.args$lty.smooth <- 1
                sel <- groups == groups.levels[j]
                smoother(u[sel], resp[sel], carPalette()[j], log.x=FALSE, log.y=FALSE, spread=FALSE,
                         smoother.args=smoother.args)
                smoother.args$lty.smooth <- 2
                smoother(u[sel], predict(model)[sel], carPalette()[j], log.x=FALSE, log.y=FALSE, spread=FALSE,
                         smoother.args=smoother.args)
            }
            items <- paste(groups.label, groups.levels, sep= " = ")
            col.items <- carPalette()[1:length(groups.levels)]
            lty.items <- 1
            if(key) plotArrayLegend(location="top",
                                    items=items, col.items=col.items,
                                    lty.items=lty.items , lwd.items=2, title="Legend")
        }
    }
    showLabels(u, resp, labels=labels,
               method=id.method, n=id.n, cex=id.cex,
               col=id.col, location=id.location)
}

mmp.glm <- function (model, variable, sd = FALSE,
                     xlab = deparse(substitute(variable)), ylab,
                     smooth=TRUE, key=TRUE, pch, groups=NULL,
                     col.line = carPalette()[c(2, 8)], col=carPalette()[1],
                     id=FALSE, grid=TRUE, ...){
    id <- applyDefaults(id, defaults=list(method="y", n=2, cex=1, col=carPalette()[1], location="lr"), type="id")
    if (isFALSE(id)){
        id.n <- 0
        id.method <- "none"
        labels <- id.cex <- id.col <- id.location <- NULL
    }
    else{
        labels <- id$labels
        if (is.null(labels)) labels <- names((residuals(model)))
        id.method <- id$method
        id.n <- if ("identify" %in% id.method) Inf else id$n
        id.cex <- id$cex
        id.col <- id$col
        id.location <- id$location
    }
    smoother.args <- applyDefaults(smooth, defaults=list(smoother=gamLine, k=3), type="smooth")
    if (!isFALSE(smoother.args)) {
        smoother <- smoother.args$smoother
        smoother.args$smoother <- NULL
    }
    else smoother <- "none"
    lwd <- match.call(expand.dots=TRUE)$lwd
    if(missing(pch)) pch <- 1
    groups.col <- col
    groups.pch <- match.call(expand.dots=TRUE)$pch
    if(is.null(groups.pch)) groups.pch <- 1
    if (!is.null(groups)){
        if(is.data.frame(groups)) {
            groups.label <- colnames(groups)[1]
            groups <- groups[,1]
        } else {
            groups.label <- deparse(substitute(groups))
        }
        groups.levels <- unique(na.omit(groups))
        for (j in 1:(length(groups.levels))) {
            pch[groups==groups.levels[j]] <- j
            groups.col[groups==groups.levels[j]] <- carPalette()[j]}
    }
    if (missing(variable)) {
        xlab <- "Linear Predictor"
        u <- predict(update(model, na.action=na.omit), type="link")
#        u <- fitted(update(model, na.action=na.omit)) #deleted 5/17/2019
    }  else {
        u <- variable }
    response <- model.response(model.frame(model))
    fam <- model$family$family
    lin <- model$family$link
    pw <- model$prior.weights # relevant only for binomial
    bernoulli <- FALSE
    if(fam == "binomial") {
        if(!any(pw > 1.1)) bernoulli <- TRUE
        if (is.factor(response)) {response <- as.numeric(response) - 1}
        if (is.matrix(response)){response <- response[, 1]/pw}
    }
    if (missing(ylab)) ylab <- colnames(model$model[1])
    plot(u, response, type="n", xlab = xlab, ylab = ylab)
    if(grid){
        grid(lty=1, equilogs=FALSE)
        box()}
    points(u, response, col=col, pch=pch, ...)
    if (!(is.character(smoother) && smoother == "none")){
        ow <- options(warn=-1)
        on.exit(options(ow))
        smoother.args$lty.smooth <-  1
        smoother.args$family <- fam
        smoother.args$link <- lin
        smoother.args$weights <- pw
        model.fit <- if(fam=="binomial") predict(model, type="response")/pw
        else predict(model, type="response")
        if(is.null(groups)) {
            smoother(u, response, col.line[1], log.x=FALSE, log.y=FALSE, spread=FALSE,
                     smoother.args=smoother.args)
            smoother.args$lty.smooth <-  2
            smoother(u, model.fit, col.line[2], log.x=FALSE, log.y=FALSE, spread=FALSE,
                     smoother.args=smoother.args)
            if(key){ outerLegend(c("Data", "Model"), lty=1:2, col=col.line,
                                 bty="n", cex=0.75, fill=col.line, border=col.line,
                                 horiz=TRUE, offset=0)
            }
        } else {
            for (j in 1:length(groups.levels)) {
                smoother.args$lwd <- if(is.null(lwd)) 1.75 else lwd
                smoother.args$lty.smooth <- 1
                sel <- groups == groups.levels[j]
                smoother(u[sel], response[sel], carPalette()[j], log.x=FALSE, log.y=FALSE,
                         spread=FALSE, smoother.args=smoother.args)
                smoother.args$lty.smooth <- 2
                smoother(u[sel], model.fit[sel], carPalette()[j], log.x=FALSE, log.y=FALSE,
                         spread=FALSE, smoother.args=smoother.args)
            }
            items <- paste(groups.label, groups.levels, sep= " = ")
            col.items <- carPalette()[1:length(groups.levels)]
            lty.items <- 1
            if(key) plotArrayLegend(location="top",
                                    items=items, col.items=col.items,
                                    lty.items=lty.items , lwd.items=2, title="Legend")
        }
    }
    showLabels(u, as.numeric(model$model[, 1]), labels=labels,
               method=id.method, n=id.n, cex=id.cex,
               col=id.col, location=id.location)
}

marginalModelPlots <- function(...) mmps(...)




mmps <- function(model, terms= ~ ., fitted=TRUE, layout=NULL, ask,
                 main, groups, key=TRUE, ...){
    mf <- if(!is.null(terms)) termsToMf(model, terms) else NULL
    labels2 <- attr(attr(mf$mf.vars, "terms"), "term.labels")
    order2 <- attr(attr(mf$mf.vars, "terms"), "order")
    type2 <- rep("good", length(labels2))
    if(length(labels2) > 0) {
        for (j in 1:length(labels2)){
            if(order2[j] > 1) type2[j] <- NA #exclude interatctions
            if(inherits(mf$mf.vars[[labels2[j]]], "factor")) type2[j] <- NA #no factors
            if(inherits(mf$mf.vars[[labels2[j]]], "matrix")) type2[j] <- "original"
        }
        if (any( type2=="original", na.rm=TRUE )){
            p1 <- try(predict(model, type="terms"), silent=TRUE)
            if(inherits(p1, "try-error")) {type2[type2=="original"] <- NA} else
                warning("Splines and/or polynomials replaced by a fitted linear combination")
        }
    }
    groups <- if (!missing(groups)) {
        termsToMf(model, as.formula(paste("~",deparse(substitute(groups)))))$mf.vars[, 2, drop=FALSE]
    } else {
        if(is.null(mf$mf.groups)) NULL else
            mf$mf.groups[, 2, drop=FALSE]
    }
    # If key=TRUE, determine the coordinates of the key:
    oma3 <- 1.5  # room for title in the outer margin ALWAYS
    mar3 <- if (is.null(groups))  1.5 else .2 +
        if(is.data.frame(groups)) length(unique(groups[, 1])) else
            length(unique(groups))
    nt <- sum(!is.na(type2)) + fitted
    if (missing(main)) main <- if (nt == 1)
        "Marginal Model Plot" else "Marginal Model Plots"
    if (nt == 0) stop("No plots specified")
    if (nt > 1 & (is.null(layout) || is.numeric(layout))) {
        if(is.null(layout)){
            layout <- switch(min(nt, 9), c(1, 1), c(1, 2), c(2, 2), c(2, 2),
                             c(3, 2), c(3, 2), c(3, 3), c(3, 3), c(3, 3))
        }
        ask <- if(missing(ask) || is.null(ask)) prod(layout)<nt else ask
    }
    op <- if(nt > 1) par(mfrow=layout, ask=ask, no.readonly=TRUE,
                         oma=c(0, 0, oma3 , 0), mar=c(5.1, 4.1, mar3, 2.1)) else
                             par(oma=c(0, 0, oma3 , 0), mar=c(5.1, 4.1, mar3, 2.1))
    on.exit(par(op))

    legend2 <- function(){
        usr <- par("usr")
        coords <-list(x=usr[1], y=usr[3])
        leg <- legend( coords, c("Data", "Model"), lty=1:2, lwd=2, bty="n",
                       cex=0.9, plot=FALSE)
        coords <- list(x = usr[2] - leg$rect$w, y=usr[4] + leg$rect$h)
        legend( coords, c("Data", "Model"), lty=1:2, lwd=2, bty="n", xpd=NA, cex=0.9)
    }
    if (length(labels2) > 0) {
        for (j in 1:length(labels2)) {
            if(!is.na(type2[j])) {
                horiz <- if(type2[j] == "original"){p1[, labels2[j]]} else {
                    if(type2[j] == "good") mf$mf.vars[ , labels2[j]] else NULL}
                lab <- labels2[j]
                mmp(model, horiz, xlab=lab, groups=groups, key=key, ...)
                if(!is.null(groups)) legend2()}
        }
    }
    if(fitted==TRUE) mmp(model, groups=groups, key=key, ...)
    if(!is.null(groups)) legend2()
    mtext(side=3, outer=TRUE, main, line=0.1, cex=1.2)
    if(any(is.na(type2))) warning("Interactions and/or factors skipped")
    invisible()
}

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