tolerance: Tolerance by _p_-value surfaces

In tilmandavies/sparr: Spatial and Spatiotemporal Relative Risk

Tolerance by p-value surfaces

Description

Calculates a p-value surface based on asymptotic theory or Monte-Carlo (MC) permutations describing the extremity of risk given a fixed or adaptive kernel-smoothed density-ratio, allowing the drawing of tolerance contours.

Usage

tolerance(
  rs,
  method = c("ASY", "MC"),
  ref.density = NULL,
  beta = 0.025,
  ITER = 100,
  parallelise = NULL,
  verbose = TRUE,
  ...
)

Arguments

rs	An object of class rrs giving the estimated relative risk function for which to calculate the p-value surface.
method	A character string specifying the method of calculation. "ASY" (default) instructs the function to compute the p-values using asymptotic theory. "MC" computes the values by random permutations of the data. See ‘Details’.
ref.density	Required if rs is based on fixed-bandwidth estimates of the case and control densities and method = "ASY". Either a pixel image or an object of class bivden giving the reference density to use in asymptotic formulae. May be unnormalised. Ignored if rs is based on adaptive kernel estimates or if method = "MC".
beta	A numeric value 0 < beta < 1 giving the fineness of the adaptive bandwidth partitioning to use for calculation of the required quantities for asymptotic adaptive p-value surfaces. Smaller values provide more accurate bandwidth bins at the cost of additional computing time, see Davies and Baddeley (2018); the default is sensible in most cases. Ignored if rs is based on fixed-bandwidth kernel estimates.
ITER	Number of iterations for the Monte-Carlo permutations. Ignored if method = "ASY".
parallelise	Numeric argument to invoke parallel processing, giving the number of CPU cores to use when method = "MC". Experimental. Test your system first using parallel::detectCores() to identify the number of cores available to you.
verbose	Logical value indicating whether to print function progress during execution.
...	Additional arguments to be passed to risk when method = "MC". While most information needed for the MC repetitions is implicitly gleaned from the object passed to rs, this ellipsis is typically used to set the appropriate epsilon and pilot.symmetry values for the internal calls to risk.

Details

This function implements developments in Hazelton and Davies (2009) (fixed) and Davies and Hazelton (2010) (adaptive) to compute pointwise p-value surfaces based on asymptotic theory of kernel-smoothed relative risk surfaces. Alternatively, the user may elect to calculate the p-value surfaces using Monte-Carlo methods (see Kelsall and Diggle, 1995). Superimposition upon a plot of the risk surface contours of these p-values at given significance levels (i.e. “tolerance contours”) can be an informative way of exploring the statistical significance of the extremity of risk across the defined study region.

Implementation of the Monte-Carlo method simply involves random allocation of case/control marks and re-estimation of the risk surface ITER times, against which the original estimate is compared. While not dependent on asymptotic theory, it is computationally expensive, and it has been suggested that it might have some undesirable practical consequences in certain settings (Hazelton and Davies, 2009). When performing the MC simulations, the same global (and pilot, if necessary) bandwidths and edge-correction regimens are employed as were used in the initial density estimates of the observed data. With regard to arguments to be passed to internal calls of risk, the user should take care to use ... to set the epsilon value to match that which was used in creation of the object passed to rs (if this was set to a non-default value). Furthermore, if performing MC simulations for the adaptive relative risk function, the function borrows the value of the beta argument to speed things up via partitioning, and the user should additionally access ... to set the same pilot.symmetry value as was used for creation of the object passed to rs, in the same way as for any non-default use of epsilon. This will ensure the simulations are all performed under the same conditions as were used to estimate the original risk function.

Value

A pixel image of the estimated p-value surface.

Note

The returned p-values are geared so that “smallness” corresponds to statistical significance of elevated risk, that is, an upper-tailed test. The complement of the p-values will yeild significance of reduced risk; a lower-tailed test. When using tol.contour, the user can control what type of contours to display.

Author(s)

T. M. Davies

References

Davies, T.M. and Baddeley A. (2018), Fast computation of spatially adaptive kernel estimates, Statistics and Computing, 28(4), 937-956.

Davies, T.M. and Hazelton, M.L. (2010), Adaptive kernel estimation of spatial relative risk, Statistics in Medicine, 29(23) 2423-2437.

Davies, T.M., Jones, K. and Hazelton, M.L. (2016), Symmetric adaptive smoothing regimens for estimation of the spatial relative risk function, Computational Statistics & Data Analysis, 101, 12-28.

Hazelton, M.L. and Davies, T.M. (2009), Inference based on kernel estimates of the relative risk function in geographical epidemiology, Biometrical Journal, 51(1), 98-109.

Kelsall, J.E. and Diggle, P.J. (1995), Kernel estimation of relative risk, Bernoulli, 1, 3-16.

Examples

data(pbc)
h0 <- LSCV.risk(pbc,method="hazelton");h0
pbccas <- split(pbc)[[1]]
pbccon <- split(pbc)[[2]]

# ASY
riskfix <- risk(pbc,h0=h0)
fixtol1 <- tolerance(riskfix,ref.density=density(pbc,OS(pbc)))

riskada <- risk(pbc,h0=h0,adapt=TRUE,hp=NS(pbc),pilot.symmetry="pooled",davies.baddeley=0.025)
adatol1 <- tolerance(riskada)

oldpar <- par(mfrow=c(1,2))
plot(riskfix)
tol.contour(fixtol1,levels=c(0.1,0.05,0.01),lty=3:1,add=TRUE)
plot(riskada)
tol.contour(adatol1,levels=c(0.1,0.05,0.01),lty=3:1,add=TRUE)
par(oldpar)

# MC
fixtol2 <- tolerance(riskfix,method="MC",ITER=200) 
adatol2 <- tolerance(riskada,method="MC",ITER=200,parallelise=2) # ~90secs with parallelisation

oldpar <- par(mfrow=c(1,2))
plot(riskfix)
tol.contour(fixtol2,levels=c(0.1,0.05,0.01),lty=3:1,add=TRUE)
plot(riskada)
tol.contour(adatol2,levels=c(0.1,0.05,0.01),lty=3:1,add=TRUE)
par(oldpar)

tilmandavies/sparr documentation built on July 8, 2024, 2:57 p.m.