R/groupSpread.R

Defines functions groupSpreadPlot groupSpread.default groupSpread.data.frame groupSpread

Documented in groupSpread groupSpread.data.frame groupSpread.default

groupSpread <-
function(xy, center=FALSE, plots=TRUE, CEPlevel=0.5, CIlevel=0.95,
         CEPtype="CorrNormal", bootCI="none", dstTarget, conversion) {
    UseMethod("groupSpread")
}

groupSpread.data.frame <-
function(xy, center=FALSE, plots=TRUE, CEPlevel=0.5, CIlevel=0.95,
         CEPtype="CorrNormal", bootCI="none", dstTarget, conversion) {
    ## distance to target from override or from data
    if(missing(dstTarget)) {
        dstTarget <- if(hasName(xy, "distance")) {
            xy[["distance"]]
        } else {
            NA_real_
        }
    }
    
    ## determine conversion factor from data if override is not given
    if(missing(conversion)) {
        conversion <- determineConversion(xy)
    }
    
    xy     <- getXYmat(xy, center=center)
    center <- FALSE                   # centering was done in getXYmat()

    groupSpread(xy, center=center, plots=plots, CEPlevel=CEPlevel,
                CIlevel=CIlevel, CEPtype=CEPtype, bootCI=bootCI,
                dstTarget=dstTarget, conversion=conversion)
    # NextMethod("groupSpread")
}

groupSpread.default <-
function(xy, center=FALSE, plots=TRUE, CEPlevel=0.5, CIlevel=0.95,
         CEPtype="CorrNormal", bootCI="none", dstTarget, conversion) {
    if(!is.matrix(xy))        { stop("xy must be a matrix") }
    if(!is.numeric(xy))       { stop("xy must be numeric") }
    if(ncol(xy) != 2L)        { stop("xy must have two columns") }
    if(!is.numeric(CEPlevel)) { stop("CEPlevel must be numeric") }
    if(CEPlevel <= 0)         { stop("CEPlevel must be > 0") }
    if(!is.numeric(CIlevel))  { stop("CIlevel must be numeric") }
    if(CIlevel <= 0)          { stop("CIlevel must be > 0") }
    if(center) {
        warning("Centering only works for data frames, ignored here")
    }

    bootCI <- match.arg(bootCI,
                        choices=c("none", "norm", "basic", "perc", "bca"),
                        several.ok=TRUE)

    ## check if CEP / CI level is given in percent
    if(CEPlevel >= 1) {
        while(CEPlevel >= 1) { CEPlevel <- CEPlevel / 100 }
        warning(paste0("CEPlevel must be in (0,1) and was set to ", CEPlevel))
    }

    if(CIlevel >= 1) {
        while(CIlevel >= 1) { CIlevel <- CIlevel / 100 }
        warning(paste0("CIlevel must be in (0,1) and was set to ", CIlevel))
    }

    dstTarget <- if(missing(dstTarget)    ||
                    all(is.na(dstTarget)) ||
                    (length(unique(dstTarget)) > 1L)) {
        NA_real_
    } else {
        mean(dstTarget)
    }
    
    conversion <- if(missing(conversion)    ||
                     all(is.na(conversion)) ||
                     (length(unique(conversion)) > 1L)) {
        NA_character_
    } else {
        unique(conversion)
    }
    
    #####-----------------------------------------------------------------------
    ## prepare data
    X    <- xy[ , 1]                     # x-coords
    Y    <- xy[ , 2]                     # y-coords
    Npts <- nrow(xy)                     # number of observations
    res  <- vector("list", 0)            # empty list to later collect the results

    ## can we do robust estimation?
    haveRobustbase <- requireNamespace("robustbase", quietly=TRUE)
    haveRob <- if(haveRobustbase && (Npts >= 4L)) {
        TRUE
    } else {
        if(Npts < 4L) {
            warning("We need >= 4 points for robust estimations")
        }
        
        if(!haveRobustbase) {
            warning("Please install package 'robustbase' for robust estimations")
        }
        
        FALSE
    }

    ## to determine axis limits later, collect all results in a vector
    axesCollX <- numeric(0)
    axesCollY <- numeric(0)

    #####-----------------------------------------------------------------------
    ## non-parametric bootstrap-CIs (basic and BCa)
    ## for all parameters where a CI is later reported
    if(!("none" %in% bootCI)) {          # do bootstrap CIs
        NrplMin <- 1499                  # minimum number of replications
        Nrpl <- if("bca" %in% bootCI) {  # number of replications
            max(NrplMin, Npts+1)         # BCa needs at least number of points
        } else {
            NrplMin
        }

        ## sdX, sdY, sigma, RSD, MR for one replication
        getSdSigRSDMR <- function(x, idx) {
            sdXY     <- sqrt(diag(cov(x[idx, ])))
            rayParam <- getRayParam(x[idx, ], level=CIlevel, doRob=FALSE)
            sigmaHat <- rayParam$sigma["sigma"]
            RSDhat   <- rayParam$RSD["RSD"]
            MRhat    <- rayParam$MR["MR"]
            return(c(sdXY, sigmaHat, RSDhat, MRhat))
        }

        bs <- boot::boot(xy, statistic=getSdSigRSDMR, R=Nrpl) # bootstrap

        ## extract CIs for all returned parameters
        sdXciBoot <- boot::boot.ci(bs, conf=CIlevel, type=bootCI, index=1)
        sdYciBoot <- boot::boot.ci(bs, conf=CIlevel, type=bootCI, index=2)
        sigCIboot <- boot::boot.ci(bs, conf=CIlevel, type=bootCI, index=3)
        RSDciBoot <- boot::boot.ci(bs, conf=CIlevel, type=bootCI, index=4)
         MRciBoot <- boot::boot.ci(bs, conf=CIlevel, type=bootCI, index=5)

        ## CI type names in output structure of boot.ci()
        CInames <- c(basic="basic", norm="normal", perc="percent", bca="bca")
        CItype  <- CInames[bootCI]
        sdXciBoot <- c(vapply(CItype, function(x) {
            len <- length(sdXciBoot[[x]])
            sdXciBoot[[x]][(len-1):len] }, numeric(2)))
        sdYciBoot <- c(vapply(CItype, function(x) {
            len <- length(sdYciBoot[[x]])
            sdYciBoot[[x]][(len-1):len] }, numeric(2)))
        sigCIboot <- c(vapply(CItype, function(x) {
            len <- length(sigCIboot[[x]])
            sigCIboot[[x]][(len-1):len] }, numeric(2)))
        RSDciBoot <- c(vapply(CItype, function(x) {
            len <- length(RSDciBoot[[x]])
            RSDciBoot[[x]][(len-1):len] }, numeric(2)))
         MRciBoot <- c(vapply(CItype, function(x) {
            len <- length(MRciBoot[[x]])
            MRciBoot[[x]][(len-1):len] }, numeric(2)))

        names(sdXciBoot) <- paste("sdX",   rep(bootCI, each=2), c("(", ")"))
        names(sdYciBoot) <- paste("sdY",   rep(bootCI, each=2), c("(", ")"))
        names(sigCIboot) <- paste("sigma", rep(bootCI, each=2), c("(", ")"))
        names(RSDciBoot) <- paste("RSD",   rep(bootCI, each=2), c("(", ")"))
        names(MRciBoot)  <- paste("MR",    rep(bootCI, each=2), c("(", ")"))
    } else {
        sdXciBoot <- numeric(0)
        sdYciBoot <- numeric(0)
        sigCIboot <- numeric(0)
        RSDciBoot <- numeric(0)
         MRciBoot <- numeric(0)
    }

    #####-----------------------------------------------------------------------
    ## standard deviations of x- and y-coords
    varXY    <- diag(cov(xy))
    sdXY     <- sqrt(varXY)
    res$sdXY <- makeMOA(sdXY, dst=dstTarget, conversion=conversion)

    ## parametric CIs for true sd
    alpha <- 1-CIlevel
    sdXci <- sqrt((Npts-1)*varXY[1] / qchisq(c(1-(alpha/2), alpha/2), Npts-1))
    sdYci <- sqrt((Npts-1)*varXY[2] / qchisq(c(1-(alpha/2), alpha/2), Npts-1))
    names(sdXci) <- c("sdX (", "sdX )")
    names(sdYci) <- c("sdY (", "sdY )")

    ## combine parametric and bootstrap CIs and add to results
    res$sdXci <- makeMOA(c(sdXci, sdXciBoot), dst=dstTarget, conversion=conversion)
    res$sdYci <- makeMOA(c(sdYci, sdYciBoot), dst=dstTarget, conversion=conversion)

    ## robust standard deviations of x- and y-coords
    res$sdXYrob <- if(haveRob) {
        rob     <- robustbase::covMcd(xy, cor=FALSE)
        sdXYrob <- sqrt(diag(rob$cov))
        makeMOA(sdXYrob, dst=dstTarget, conversion=conversion)
    } else {
        NULL
    }                                    # if(haveRob)

    ## (robust) center and covariance-matrix
    ctr <- colMeans(xy)                  # group center
    ctrRob <- if(haveRob) {
        rob$center
    } else {
        NULL
    }                                    # if(haveRob)

    res$covXY <- cov(xy)                 # covariance matrix
    res$covXYrob <- if(haveRob) {
        rob$cov
    } else {
        NULL
    }                                    # if(haveRob)

    #####-----------------------------------------------------------------------
    ## mean distance to group center and associated parameterss
    dstCtr     <- getDistToCtr(xy)
    dstCtrMean <- mean(dstCtr)
    dstCtrMed  <- median(dstCtr)
    dstCtrMax  <- max(dstCtr)

    ## radial standard deviation
    ## http://ballistipedia.com/index.php?title=Describing_Precision
    rayParam <- getRayParam(xy, level=CIlevel, doRob=FALSE)

    ## sigma, RSD, MR estimates with parametric confidence intervals
    sigma <- rayParam$sigma
    RSD   <- rayParam$RSD
    MR    <- rayParam$MR

    names(sigma) <- c("sigma", "sigma (", "sigma )")
    names(RSD)   <- c("RSD",   "RSD (",   "RSD )")
    names(MR)    <- c("MR",    "MR (",    "MR )")

    mDTCsigRSDmr  <- c(mean=dstCtrMean, median=dstCtrMed, max=dstCtrMax,
                       sigma["sigma"], RSD["RSD"], MR["MR"])
    res$distToCtr <- makeMOA(mDTCsigRSDmr, dst=dstTarget, conversion=conversion)

    ## combine parametric and bootstrap CIs and add to results
    sigmaCI     <- c(sigma[c("sigma (", "sigma )")], sigCIboot)
    res$sigmaCI <- makeMOA(sigmaCI, dst=dstTarget, conversion=conversion)

    RSDci     <- c(RSD[c("RSD (", "RSD )")], RSDciBoot)
    res$RSDci <- makeMOA(RSDci, dst=dstTarget, conversion=conversion)

    MRci     <- c(MR[c("MR (", "MR )")], MRciBoot)
    res$MRci <- makeMOA(MRci, dst=dstTarget, conversion=conversion)

    #####-----------------------------------------------------------------------
    ## maximum pairwise distance
    maxPD <- getMaxPairDist(xy)
    res$maxPairDist <- makeMOA(maxPD$d, dst=dstTarget, conversion=conversion)

    #####-----------------------------------------------------------------------
    ## width, height, FoM, diagonal of (minimum) bounding box
    bb    <- getBoundingBox(xy)          # bounding box
    bbMin <- getMinBBox(xy)              # minimum bounding box
    groupRect    <- c(width=bb$width,    height=bb$height,    FoM=bb$FoM,    diag=bb$diag)
    groupRectMin <- c(width=bbMin$width, height=bbMin$height, FoM=bbMin$FoM, diag=bbMin$diag)

    res$groupRect    <- makeMOA(groupRect,    dst=dstTarget, conversion=conversion)
    res$groupRectMin <- makeMOA(groupRectMin, dst=dstTarget, conversion=conversion)

    ## for axis limits
    axesCollX <- c(axesCollX, bb$pts[c(1, 3)], bbMin$pts[ , 1])
    axesCollY <- c(axesCollY, bb$pts[c(2, 4)], bbMin$pts[ , 2])

    #####-----------------------------------------------------------------------
    ## radius of minimum enclosing circle
    minCirc <- getMinCircle(xy)          # minimum enclosing circle
    res$minCircleRad <- makeMOA(minCirc$rad, dst=dstTarget, conversion=conversion)

    ## for axis limits
    axesCollX <- c(axesCollX, minCirc$ctr[1] + minCirc$rad,
                              minCirc$ctr[1] - minCirc$rad)
    axesCollY <- c(axesCollY, minCirc$ctr[2] + minCirc$rad,
                              minCirc$ctr[2] - minCirc$rad)

    #####-----------------------------------------------------------------------
    ## radii of minimum enclosing ellipse
    minEll <- getMinEllipse(xy)          # minimum enclosing circle
    res$minEll <- t(rbind(semi_major=makeMOA(minEll$size[1], dst=dstTarget, conversion=conversion),
                          semi_minor=makeMOA(minEll$size[2], dst=dstTarget, conversion=conversion)))
    
    #####-----------------------------------------------------------------------
    ## confidence ellipse measures
    confEll     <- getConfEll(xy, CEPlevel, dstTarget=dstTarget,
                              conversion=conversion, doRob=haveRob)
    res$confEll <- confEll$size

    ## for axis limits
    axesCollX <- c(axesCollX, confEll$ctr[1] + confEll$size["unit", "semi-major"],
                              confEll$ctr[1] - confEll$size["unit", "semi-major"])
    axesCollY <- c(axesCollY, confEll$ctr[2] + confEll$size["unit", "semi-major"],
                              confEll$ctr[2] - confEll$size["unit", "semi-major"])

    if(haveRob) {
        res$confEllRob <- confEll$sizeRob

        ## for axis limits
        axesCollX <- c(axesCollX, confEll$ctrRob[1] + confEll$sizeRob["unit", "semi-major"],
                                  confEll$ctrRob[1] - confEll$sizeRob["unit", "semi-major"])
        axesCollY <- c(axesCollY, confEll$ctrRob[2] + confEll$sizeRob["unit", "semi-major"],
                                  confEll$ctrRob[2] - confEll$sizeRob["unit", "semi-major"])
    } else {
        res$confEllRob <- NULL
    }                                    # if(haveRob)

    res$confEllShape    <- confEll$shape
    res$confEllShapeRob <- if(haveRob) {
        confEll$shapeRob
    } else {
        NULL
    }                                    # if(haveRob)

    #####-----------------------------------------------------------------------
    ## circular error probable
    CEP <- getCEP(xy, CEPlevel=CEPlevel, type=CEPtype, dstTarget=dstTarget,
                  conversion=conversion, doRob=FALSE)
    res$CEP <- CEP$CEP

    #####-----------------------------------------------------------------------
    ## plotting
    if(plots) {
        ## infer (x,y)-coord units from conversion
        unitXY  <- na.omit(getUnits(conversion, first=FALSE))
        unitDst <- na.omit(getUnits(conversion, first=TRUE))
        devNew  <- getDevice()           # platform-dependent window open

        ## distance to target may be heterogeneous
        dstTargetPlot <- paste(unique(round(na.omit(dstTarget))), collapse=", ")

        #####-------------------------------------------------------------------
        ## diagram: histogram for distances to group center
        ## Rayleigh fit and kernel density estimate
        xRange    <- range(dstCtr)
        xPts      <- seq(xRange[1], xRange[2], length.out=200)
        yRayleigh <- dRayleigh(xPts, sigma["sigma"])
        yKDE      <- density(dstCtr)

        devNew()                         # open new diagram
        h <- hist(dstCtr, breaks="FD", plot=FALSE)
        plot(h, freq=FALSE,
             main="Histogram distances to center w/ kernel density estimate",
             sub=paste("distance:", dstTargetPlot, unitDst),
             xlab=paste0("distance [", unitXY, "]"),
             ylim=c(0, max(c(h$density, yRayleigh, yKDE$y))))

        rug(jitter(dstCtr))              # show single values

        ## add Rayleigh fit and kernel density estimate
        lines(xPts,   yRayleigh, lwd=2, col="blue")
        lines(yKDE$x, yKDE$y,    lwd=2, col="red")
        legend(x="topright",
               legend=c("Rayleigh distribution", "kernel density estimate"),
               col=c("blue", "red"), lty=1, lwd=2, bg=rgb(1, 1, 1, 0.7))

        #####-------------------------------------------------------------------
        ## diagram: 2D-scatter plot for the (x,y)-distribution
        ## determine axis limits
        xLims <- range(c(X, axesCollX))
        yLims <- range(c(Y, axesCollY))

        devNew()                           # open new diagram
        plot(Y ~ X, asp=1, xlim=xLims, ylim=yLims, pch=20,
             main="Group (x,y)-coordinates",
             sub=paste("distance:", dstTargetPlot, unitDst),
             xlab=paste0("X [", unitXY, "]"), ylab=paste0("Y [", unitXY, "]"))
        abline(v=0, h=0, col="lightgray")  # add point of aim

        ## add group center and robust estimate for group center
        points(ctr[1], ctr[2], col="red",  pch=4, lwd=2, cex=1.5)
        if(haveRob) {
            points(ctrRob[1], ctrRob[2], col="blue", pch=4, lwd=2, cex=1.5)
        }                                # if(haveRob)

        ## add confidence ellipses (parametric, robust),
        ## and a circle with mean distance to center
        drawEllipse(confEll, pch=4, fg="red", lwd=2)
        if(haveRob) {
            drawEllipse(ctrRob, res$covXYrob, radius=confEll$magFac,
                        pch=4, fg="blue", lwd=2)
        }                                # if(haveRob)
        drawCircle(ctr, radius=mean(dstCtr), fg="black", lwd=2)

        ## add legend
        legend(x="bottomleft", legend=c("center", "center (robust)",
               paste(100*CEPlevel, "% confidence ellipse", sep=""),
               paste(100*CEPlevel, "% confidence ellipse (robust)", sep=""),
               "mean distance to center"),
               col=c("red", "blue", "red", "blue", "black"),
               pch=c(4, 4, NA, NA, NA),
               lty=c(NA, NA, 1, 1, 1), lwd=2, bg=rgb(1, 1, 1, 0.7))

        #####-------------------------------------------------------------------
        ## diagram: 2D-scatter plot for the (x,y)-distribution
        devNew()                         # open new diagram
        plot(Y ~ X, asp=1, xlim=xLims, ylim=yLims, pch=20,
             main="Group (x,y)-coordinates",
             sub=paste("distance:", dstTargetPlot, unitDst),
             xlab=paste0("X [", unitXY, "]"), ylab=paste0("Y [", unitXY, "]"))
        abline(v=0, h=0, col="lightgray")                            # add point of aim
        points(ctr[1], ctr[2], col="gray40", pch=4, lwd=4, cex=2.5)  # add group center

        ## add bounding box, minimum bounding box, minimum enclosing circle,
        ## and maximum group spread
        drawBox(bb, fg="magenta", lwd=2)
        drawBox2(bbMin, fg="red", lwd=2)
        drawCircle(minCirc, fg="blue", lwd=2)
        segments(x0=xy[maxPD$idx[1], 1], y0=xy[maxPD$idx[1], 2],
                 x1=xy[maxPD$idx[2], 1], y1=xy[maxPD$idx[2], 2],
                 col="green3", lwd=2)

        ## add legend
        legend(x="bottomleft", legend=c("group center", "bounding box",
               "minimum bounding box",
               "minimum enclosing circle", "maximum group spread"),
               col=c("gray40", "magenta", "red", "blue", "green3"),
               pch=c(4, NA, NA, NA, NA), lty=c(NA, 1, 1, 1, 1), lwd=2,
               bg=rgb(1, 1, 1, 0.7))
    }                                    # if(plots)

    #####-----------------------------------------------------------------------
    ## return all the collected numerical results and tests
    return(res)
}

groupSpreadPlot <-
function(xy, which=1L, center=FALSE, CEPlevel=0.5, CIlevel=0.95,
         dstTarget, conversion) {
    if(!is.data.frame(xy))    { stop("xy must be a data.frame") }
    xy <- getXYmat(xy, center=center)
    if(!is.numeric(CEPlevel)) { stop("CEPlevel must be numeric") }
    if(CEPlevel <= 0)         { stop("CEPlevel must be > 0") }
    if(!is.numeric(CIlevel))  { stop("CIlevel must be numeric") }
    if(CIlevel <= 0)          { stop("CIlevel must be > 0") }

    which <- match.arg(as.character(which), choices=1:4)

    ## check if CEP / CI level is given in percent
    if(CIlevel >= 1) {
        while(CIlevel >= 1) { CIlevel <- CIlevel / 100 }
        warning(c("CIlevel must be in (0,1) and was set to ", CIlevel))
    }

    if(CEPlevel >= 1) {
        while(CEPlevel >= 1) { CEPlevel <- CEPlevel / 100 }
        warning(c("CEPlevel must be in (0,1) and was set to ", CEPlevel))
    }

    dstTarget <- if(missing(dstTarget)    ||
                    all(is.na(dstTarget)) ||
                    (length(unique(dstTarget)) > 1L)) {
        NA_real_
    } else {
        mean(dstTarget)
    }
    
    conversion <- if(missing(conversion)    ||
                     all(is.na(conversion)) ||
                     (length(unique(conversion)) > 1L)) {
        NA_character_
    } else {
        unique(conversion)
    }
    
    #####-----------------------------------------------------------------------
    ## prepare data
    X    <- xy[ , 1]                     # x-coords
    Y    <- xy[ , 2]                     # y-coords
    Npts <- nrow(xy)                     # number of observations
    res  <- vector("list", 0)            # empty list to later collect the results

    ## can we do robust estimation?
    haveRobustbase <- requireNamespace("robustbase", quietly=TRUE)
    haveRob <- if(haveRobustbase && (Npts >= 4L)) {
        TRUE
    } else {
        if(Npts < 4L) {
            warning("We need >= 4 points for robust estimations")
        }
        
        if(!haveRobustbase) {
            warning("Please install package 'robustbase' for robust estimations")
        }
        
        FALSE
    }
    
    ## to determine axis limits later, collect all results in a vector
    axesCollX <- numeric(0)
    axesCollY <- numeric(0)

    #####-----------------------------------------------------------------------
    ## standard deviations of x- and y-coords
    varXY    <- diag(cov(xy))
    sdXY     <- sqrt(varXY)

    ## robust standard deviations of x- and y-coords
    if(haveRob) {
        rob <- robustbase::covMcd(xy, cor=FALSE)
        sdXYrob <- sqrt(diag(rob$cov))
    }                                  # if(haveRob)

    ## (robust) center and covariance-matrix
    ctr <- colMeans(xy)                  # group center
    if(haveRob) {
        ctrRob <- rob$center
    }                                    # if(haveRob)

    res$covXY <- cov(xy)                 # covariance matrix

    if(haveRob) {
        res$covXYrob <- rob$cov
    }                                    # if(haveRob)

    #####-----------------------------------------------------------------------
    ## mean distance to group center and associated parameterss
    dstCtr <- getDistToCtr(xy)

    ## radial standard deviation
    ## http://ballistipedia.com/index.php?title=Describing_Precision
    rayParam <- getRayParam(xy, level=CIlevel, doRob=FALSE)

    ## sigma, RSD, MR estimates with parametric confidence intervals
    sigma <- rayParam$sigma
    names(sigma) <- c("sigma", "sigma (", "sigma )")

    #####-----------------------------------------------------------------------
    ## maximum pairwise distance
    maxPD <- getMaxPairDist(xy)
    res$maxPairDist <- makeMOA(maxPD$d, dst=dstTarget, conversion=conversion)

    #####-----------------------------------------------------------------------
    ## width, height, FoM, diagonal of (minimum) bounding box
    bb    <- getBoundingBox(xy)          # bounding box
    bbMin <- getMinBBox(xy)              # minimum bounding box

    ## for axis limits
    axesCollX <- c(axesCollX, bb$pts[c(1, 3)], bbMin$pts[ , 1])
    axesCollY <- c(axesCollY, bb$pts[c(2, 4)], bbMin$pts[ , 2])

    #####-----------------------------------------------------------------------
    ## radius of minimum enclosing circle
    minCirc <- getMinCircle(xy)          # minimum enclosing circle

    ## for axis limits
    axesCollX <- c(axesCollX, minCirc$ctr[1] + minCirc$rad,
                              minCirc$ctr[1] - minCirc$rad)
    axesCollY <- c(axesCollY, minCirc$ctr[2] + minCirc$rad,
                              minCirc$ctr[2] - minCirc$rad)

    #####-----------------------------------------------------------------------
    ## confidence ellipse measures
    confEll <- getConfEll(xy, CEPlevel, dstTarget=dstTarget,
                          conversion=conversion, doRob=haveRob)

    ## for axis limits
    axesCollX <- c(axesCollX, confEll$ctr[1] + confEll$size["unit", "semi-major"],
                              confEll$ctr[1] - confEll$size["unit", "semi-major"])
    axesCollY <- c(axesCollY, confEll$ctr[2] + confEll$size["unit", "semi-major"],
                              confEll$ctr[2] - confEll$size["unit", "semi-major"])

    #####-----------------------------------------------------------------------
    ## minimum enclosing ellipse measures
    minEll <- getMinEllipse(xy)

    ## for axis limits
    axesCollX <- c(axesCollX,
                   minEll$ctr[1] + minEll$size[1],
                   minEll$ctr[1] - minEll$size[1])
    axesCollY <- c(axesCollY,
                   minEll$ctr[2] + minEll$size[1],
                   minEll$ctr[2] - minEll$size[1])
    
    if(haveRob) {
        res$confEllRob <- confEll$sizeRob

        ## for axis limits
        axesCollX <- c(axesCollX, confEll$ctrRob[1] + confEll$sizeRob["unit", "semi-major"],
                                  confEll$ctrRob[1] - confEll$sizeRob["unit", "semi-major"])
        axesCollY <- c(axesCollY, confEll$ctrRob[2] + confEll$sizeRob["unit", "semi-major"],
                                  confEll$ctrRob[2] - confEll$sizeRob["unit", "semi-major"])
    }                                    # if(haveRob)

    #####-----------------------------------------------------------------------
    ## plotting
    ## infer (x,y)-coord units from conversion
    unitXY  <- na.omit(getUnits(conversion, first=FALSE))
    unitDst <- na.omit(getUnits(conversion, first=TRUE))

    ## determine axis limits
    xLims <- range(c(X, axesCollX))
    yLims <- range(c(Y, axesCollY))

    ## distance to target may be heterogeneous
    dstTargetPlot <- paste(unique(round(na.omit(dstTarget))), collapse=", ")
    
    if(which == 1L) {
        #####-------------------------------------------------------------------
        ## diagram: histogram for distances to group center
        xRange    <- range(dstCtr)
        xPts      <- seq(xRange[1], xRange[2], length.out=200)
        yRayleigh <- dRayleigh(xPts, sigma["sigma"])
        yKDE      <- density(dstCtr)

        h <- hist(dstCtr, breaks="FD", plot=FALSE)
        plot(h, freq=FALSE,
             main="Histogram distances to center w/ kernel density estimate",
             sub=paste("distance:", dstTargetPlot, unitDst),
             xlab=paste0("distance [", unitXY, "]"),
             ylim=c(0, max(c(h$density, yRayleigh, yKDE$y))))

        rug(jitter(dstCtr))              # show single values

        ## add Rayleigh fit and kernel density estimate
        lines(xPts,   yRayleigh, lwd=2, col="blue")
        lines(yKDE$x, yKDE$y,    lwd=2, col="red")
        legend(x="topright",
               legend=c("Rayleigh distribution", "kernel density estimate"),
               col=c("blue", "red"), lty=1, lwd=2, bg=rgb(1, 1, 1, 0.7))
    }

    if(which == 2L) {
        #####-------------------------------------------------------------------
        ## diagram: 2D-scatter plot for the (x,y)-distribution
        plot(Y ~ X, asp=1, xlim=xLims, ylim=yLims, pch=20,
             main="Group (x,y)-coordinates",
             sub=paste("distance:", dstTargetPlot, unitDst),
             xlab=paste0("X [", unitXY, "]"), ylab=paste0("Y [", unitXY, "]"))
        abline(v=0, h=0, col="lightgray")  # add point of aim

        ## add group center and robust estimate for group center
        points(ctr[1], ctr[2], col="red",  pch=4, lwd=2, cex=1.5)
        if(haveRob) {
            points(ctrRob[1], ctrRob[2], col="blue", pch=4, lwd=2, cex=1.5)
        }                                # if(haveRob)

        ## add confidence ellipses (parametric, robust),
        ## and a circle with mean distance to center
        drawEllipse(confEll, pch=4, fg="red", lwd=2)
        if(haveRob) {
            drawEllipse(ctrRob, res$covXYrob, radius=confEll$magFac,
                        pch=4, fg="blue", lwd=2)
        }                                # if(haveRob)
        drawCircle(ctr, radius=mean(dstCtr), fg="black", lwd=2)

        ## add legend
        legend(x="bottomleft", legend=c("center", "center (robust)",
               paste(100*CEPlevel, "% confidence ellipse", sep=""),
               paste(100*CEPlevel, "% confidence ellipse (robust)", sep=""),
               "mean distance to center"),
               col=c("red", "blue", "red", "blue", "black"),
               pch=c(4, 4, NA, NA, NA),
               lty=c(NA, NA, 1, 1, 1), lwd=2, bg=rgb(1, 1, 1, 0.7))
    }

    if(which == 3L) {
        #####-------------------------------------------------------------------
        ## diagram: 2D-scatter plot for the (x,y)-distribution
        plot(Y ~ X, asp=1, xlim=xLims, ylim=yLims, pch=20,
             main="Group (x,y)-coordinates",
             sub=paste("distance:", dstTargetPlot, unitDst),
             xlab=paste0("X [", unitXY, "]"), ylab=paste0("Y [", unitXY, "]"))
        abline(v=0, h=0, col="lightgray")                            # add point of aim
        points(ctr[1], ctr[2], col="gray40", pch=4, lwd=4, cex=2.5)  # add group center

        ## add bounding box, minimum bounding box, and maximum group spread
        drawBox(bb, fg="magenta", lwd=2)
        drawBox2(bbMin, fg="red", lwd=2)
        segments(x0=xy[maxPD$idx[1], 1], y0=xy[maxPD$idx[1], 2],
                 x1=xy[maxPD$idx[2], 1], y1=xy[maxPD$idx[2], 2],
                 col="blue", lwd=2)

        ## add legend
        legend(x="bottomleft",
               legend=c("group center",
                        "bounding box",
                        "minimum bounding box",
                        "maximum group spread"),
               col=c("gray40", "magenta", "red", "blue"),
               pch=c(4, NA, NA, NA),
               lty=c(NA, 1, 1, 1),
               lwd=2,
               bg=rgb(1, 1, 1, 0.7))
    }                                    # if(plots)

    if(which == 4L) {
        #####-------------------------------------------------------------------
        ## diagram: 2D-scatter plot for the (x,y)-distribution
        plot(Y ~ X, asp=1, xlim=xLims, ylim=yLims, pch=20,
             main="Group (x,y)-coordinates",
             sub=paste("distance:", dstTargetPlot, unitDst),
             xlab=paste0("X [", unitXY, "]"), ylab=paste0("Y [", unitXY, "]"))
        abline(v=0, h=0, col="lightgray")                            # add point of aim
        points(ctr[1], ctr[2], col="gray40", pch=4, lwd=4, cex=2.5)  # add group center
        
        ## add minimum enclosing circle, minimum enclosing ellipse,
        ## and maximum group spread
        drawCircle(minCirc, fg="magenta", lwd=2)
        drawEllipse(minEll, fg="red", lwd=2)
        segments(x0=xy[maxPD$idx[1], 1], y0=xy[maxPD$idx[1], 2],
                 x1=xy[maxPD$idx[2], 1], y1=xy[maxPD$idx[2], 2],
                 col="blue", lwd=2)
        
        ## add legend
        legend(x="bottomleft",
               legend=c("group center",
                        "minimum enclosing circle",
                        "minimum enclosing ellipse",
                        "maximum group spread"),
               col=c("gray40", "magenta", "red", "blue"),
               pch=c(4, NA, NA, NA),
               lty=c(NA, 1, 1, 1),
               lwd=2,
               bg=rgb(1, 1, 1, 0.7))
    }                                    # if(plots)
    
    #####-----------------------------------------------------------------------
    ## return all the collected numerical results and tests
    return(invisible(NULL))
}
dwoll/shotGroups documentation built on Feb. 16, 2024, 2:21 p.m.