README

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DSSP

The goal of DSSP is to draw samples from the direct sampling spatial prior model (DSSP) described in White et. al. 2019. The basic model assumes a Gaussian likelihood and derives a spatial prior based on thin-plate splines. Functions are included so that the model can be extended to be used for generalised linear mixed models or Bayesian Hierarchical Models.

Installation

# install.packages("devtools")
devtools::install_github("gentrywhite/DSSP")

Example

data("meuse.all", package = "gstat")
sp::coordinates(meuse.all) <- ~ x + y

This model does includes two covariates and their posterior densities are summarised in the summary()

library(DSSP)
meuse.fit <- DSSP(
  formula = log(zinc) ~ log(lead) + lime, data = meuse.all, N = 10000,
  pars = c(0.001, 0.001), log_prior = function(x) -2 * log(1 + x)
)
summary(meuse.fit)
#> Formula: log(zinc) ~ log(lead) + lime
#> Number of observations: 164
#> Number of iterations: 10000
#> 
#> Summary of model:
#>       Estimate Est.Error l-95% CI u-95% CI      ESS
#> eta     334.14   1202.47     3.61  1897.49 10000.00
#> delta     0.11      0.01     0.09     0.14 10000.00
#> 
#> Summary of covariates:
#>             Estimate Est.Error  min q0.025 q0.25 q0.50 q0.75 q0.975  max
#> (Intercept)     1.25      0.20 0.48   0.89  1.12  1.25  1.38   1.67 2.30
#> log(lead)       0.96      0.04 0.84   0.89  0.94  0.96  0.99   1.03 1.10
#> lime            0.24      0.05 0.03   0.14  0.20  0.24  0.27   0.34 0.43

plot(meuse.fit)
#> `geom_smooth()` using formula 'y ~ x'

Introduction

The Direct Sampling Spatial Prior (DSSP) is based on the thin-plate splines solution to the smoothing problem of minimising the penalised sum of squares

[ S_{\eta}(f) = \frac{1}{n}\sum^{n}_{i}W_i(y_i - f(\mathbf{x}_i))^2 +\eta J_m(f)](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%0AS_%7B%5Ceta%7D%28f%29%20%3D%20%5Cfrac%7B1%7D%7Bn%7D%5Csum%5E%7Bn%7D_%7Bi%7DW_i%28y_i%20-%20f%28%5Cmathbf%7Bx%7D_i%29%29%5E2%0A%2B%5Ceta%20J_m%28f%29%0A ” S_{}(f) = ^{n}_{i}W_i(y_i - f(_i))^2 +J_m(f) “)

[ \min_{\mathbf{\nu}}\:(\mathbf{y}-\mathbf{\nu})‘\mathbf{W}(\mathbf{y}-\mathbf{\nu})+ \eta\mathbf{\nu}’\mathbf{M}\mathbf{\nu}.](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%0A%5Cmin_%7B%5Cmathbf%7B%5Cnu%7D%7D%5C%3A%28%5Cmathbf%7By%7D-%5Cmathbf%7B%5Cnu%7D%29%27%5Cmathbf%7BW%7D%28%5Cmathbf%7By%7D-%5Cmathbf%7B%5Cnu%7D%29%2B%0A%5Ceta%5Cmathbf%7B%5Cnu%7D%27%5Cmathbf%7BM%7D%5Cmathbf%7B%5Cnu%7D.%0A ” _{}:(-)‘(-)+ ’. “)

[ \hat{\mathbf{\nu}}= (\mathbf{W}+\eta\mathbf{M})^{-1}\mathbf{y}.](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%0A%5Chat%7B%5Cmathbf%7B%5Cnu%7D%7D%3D%0A%28%5Cmathbf%7BW%7D%2B%5Ceta%5Cmathbf%7BM%7D%29%5E%7B-1%7D%5Cmathbf%7By%7D.%0A ” = (+)^{-1}. “)

[ \mathbf{y}\sim N(\mathbf{\nu},\delta\mathbf{W}^{-1})](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%0A%5Cmathbf%7By%7D%5Csim%20N%28%5Cmathbf%7B%5Cnu%7D%2C%5Cdelta%5Cmathbf%7BW%7D%5E%7B-1%7D%29%0A ” N(,^{-1}) “)

[ \left[\mathbf{\nu}\mid\eta,\delta\right]\propto\ \frac{\eta}{\delta}^{-{r}/2} \exp\left(-\frac{\eta}{2\delta}\mathbf{\nu}’\mathbf{M}\mathbf{\nu}\right),](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%0A%5Cleft%5B%5Cmathbf%7B%5Cnu%7D%5Cmid%5Ceta%2C%5Cdelta%5Cright%5D%5Cpropto%5C%20%5Cfrac%7B%5Ceta%7D%7B%5Cdelta%7D%5E%7B-%7Br%7D%2F2%7D%0A%5Cexp%5Cleft%28-%5Cfrac%7B%5Ceta%7D%7B2%5Cdelta%7D%5Cmathbf%7B%5Cnu%7D%27%5Cmathbf%7BM%7D%5Cmathbf%7B%5Cnu%7D%5Cright%29%2C%0A ” ^{-{r}/2} (-’), “)

[ -\frac{1}{2\delta}\left( (\mathbf{y}-\mathbf{\nu})‘\mathbf{W}({\mathbf{y}}-\mathbf{\nu}) -\eta\mathbf{\nu}’\mathbf{M}\mathbf{\nu}\right)](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%0A-%5Cfrac%7B1%7D%7B2%5Cdelta%7D%5Cleft%28%20%28%5Cmathbf%7By%7D-%5Cmathbf%7B%5Cnu%7D%29%27%5Cmathbf%7BW%7D%28%7B%5Cmathbf%7By%7D%7D-%5Cmathbf%7B%5Cnu%7D%29%0A-%5Ceta%5Cmathbf%7B%5Cnu%7D%27%5Cmathbf%7BM%7D%5Cmathbf%7B%5Cnu%7D%5Cright%29%0A ” -( (-)‘({}-) -’) “)

which yields the posterior mean with the same solution as the penalised least squares.

The complete model is specified with a Gaussian likelihood, the improper prior for $\nu$ , an inverse gaussian prior for $\delta$ , and a prior for $\eta$ . With this specification the joint posterior is written

[ \pi\left(\mathbf{\nu},\delta_0,\eta|\mathbf{y}\right)\propto f(\mathbf{y}|\mathbf{\nu},\delta)\pi\left(\mathbf{\nu}|\eta,\delta\right)\pi\left(\delta\right) \pi\left(\eta\right).](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%0A%5Cpi%5Cleft%28%5Cmathbf%7B%5Cnu%7D%2C%5Cdelta_0%2C%5Ceta%7C%5Cmathbf%7By%7D%5Cright%29%5Cpropto%0Af%28%5Cmathbf%7By%7D%7C%5Cmathbf%7B%5Cnu%7D%2C%5Cdelta%29%5Cpi%5Cleft%28%5Cmathbf%7B%5Cnu%7D%7C%5Ceta%2C%5Cdelta%5Cright%29%5Cpi%5Cleft%28%5Cdelta%5Cright%29%0A%5Cpi%5Cleft%28%5Ceta%5Cright%29.%0A ” (,_0,|) f(|,)(|,)() (). “)

which can be sampled directly in sequence to create a draw from the joint posterior

[ \pi\left(\mathbf{\nu},\delta_0,\eta|\mathbf{y}\right).](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%0A%5Cpi%5Cleft%28%5Cmathbf%7B%5Cnu%7D%2C%5Cdelta_0%2C%5Ceta%7C%5Cmathbf%7By%7D%5Cright%29.%0A ” (,_0,|). “)

see G. White, D. Sun, P. Speckman (2019) <arXiv:1906.05575> for details↩︎

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.