R/twinstim_siaf_student.R

In surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

################################################################################
### Student (t) kernel f(s) = (||s||^2+sigma^2)^-d
### This is a reparametrization of the t-kernel; For d=1, this is the kernel of
### the Cauchy density with scale sigma; in Geostatistics, a correlation
### function of this kind is known as the Cauchy model.
###
### Copyright (C) 2013-2014,2017 Sebastian Meyer
###
### This file is part of the R package "surveillance",
### free software under the terms of the GNU General Public License, version 2,
### a copy of which is available at https://www.R-project.org/Licenses/.
################################################################################


siaf.student <- function (nTypes = 1, validpars = NULL, engine = "C")
{
    nTypes <- as.integer(nTypes)
    stopifnot(length(nTypes) == 1L, nTypes > 0L)
    engine <- match.arg(engine, c("C", "R"))

    ## for the moment we don't make this type-specific
    if (nTypes != 1) stop("type-specific shapes are not yet implemented")

    ## helper expression, note: logpars=c(logscale=logsigma, logd=logd)
    tmp <- expression(
        logsigma <- logpars[[1L]],  # used "[[" to drop names
        logd <- logpars[[2L]],
        sigma <- exp(logsigma),
        d <- exp(logd)
        )

    ## spatial kernel
    f <- function (s, logpars, types = NULL) {}
    body(f) <- as.call(c(as.name("{"),
        tmp,
        expression(s2 <- .rowSums(s^2, nrow(s), 2L)),
        expression((s2+sigma^2)^-d)
    ))
    environment(f) <- baseenv()

    ## numerically integrate f over a polygonal domain
    F <- siaf_F_polyCub_iso(intrfr_name = "intrfr.student", engine = engine)

    ## fast integration of f over a circular domain
    ## is not relevant for this heavy-tail kernel since we don't use
    ## 'effRange', and usually eps.s=Inf
    ##Fcircle <- function (r, logpars, type = NULL) {}

    ## derivative of f wrt logpars
    deriv <- f
    body(deriv)[[length(body(deriv))]] <- # assignment for return value of f
        substitute(fvals <- x, list(x=body(deriv)[[length(body(deriv))]]))
    body(deriv) <- as.call(c(as.list(body(deriv)), expression(
        derivlogsigma <- -2*d*sigma^2 * fvals / (s2+sigma^2),
        derivlogd <- log(fvals) * fvals,
        cbind(derivlogsigma, derivlogd, deparse.level = 0)
        )))
    environment(deriv) <- baseenv()

    ## Numerical integration of 'deriv' over a polygonal domain
    Deriv <- siaf_Deriv_polyCub_iso(
        intrfr_names = c("intrfr.student.dlogsigma", "intrfr.student.dlogd"),
        engine = engine)

    ## simulation from the kernel (via polar coordinates)
    simulate <- siaf.simulatePC(intrfr.student)
    environment(simulate) <- getNamespace("surveillance")

    ## return the kernel specification
    list(f=f, F=F, deriv=deriv, Deriv=Deriv, simulate=simulate,
         npars=2L, validpars=validpars)
}


## integrate x*f(x) from 0 to R (vectorized)
intrfr.student <- function (R, logpars, types = NULL)
{
    sigma <- exp(logpars[[1L]])
    d <- exp(logpars[[2L]])
    if (d == 1) {
        log(R^2+sigma^2) / 2 - log(sigma)
    } else {
        ( (R^2+sigma^2)^(-d+1) - (sigma^2)^(-d+1) ) / (2-2*d)
    }
}

## integrate x * (df(x)/dlogsigma) from 0 to R (vectorized)
intrfr.student.dlogsigma <- function (R, logpars, types = NULL)
{
    sigma <- exp(logpars[[1L]])
    d <- exp(logpars[[2L]])
    sigma^2 * ( (R^2+sigma^2)^-d - sigma^(-2*d) )
}

## integrate x * (df(x)/dlogd) from 0 to R (vectorized)
intrfr.student.dlogd <- function (R, logpars, types = NULL)
{
    sigma <- exp(logpars[[1L]])
    d <- exp(logpars[[2L]])
    if (d == 1) {
        log(sigma)^2 - log(R^2+sigma^2)^2 / 4
    } else { # thanks to Maple 17
        primitive <- function (x) {
            x2ps2 <- x^2 + sigma^2
            (d*(d-1)*log(x2ps2) + d) / (2*(d-1)^2 * (x2ps2)^(d-1))
        }
        primitive(R) - primitive(0)
    }
}