Help for package spTDyn

Type:

Package

Title:

Spatially Varying and Spatio-Temporal Dynamic Linear Models

Version:

2.0.3

Date:

2024-09-09

Depends:

R (≥ 4.4.0), spTimer

Description:

Fits, spatially predicts, and temporally forecasts space-time data using Gaussian Process (GP): (1) spatially varying coefficient process models and (2) spatio-temporal dynamic linear models. Bakar et al., (2016). Bakar et al., (2015).

Imports:

coda, sp, spacetime, grDevices, graphics, stats, utils

License:

GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]

LazyData:

yes

NeedsCompilation:

yes

Packaged:

2024-09-09 01:18:27 UTC; kbak4671

Author:

K. Shuvo Bakar

[aut, cre], Philip Kokic [ctb], Huidong Jin

[ctb]

Maintainer:

K. Shuvo Bakar <shuvo.bakar@gmail.com>

Repository:

CRAN

Date/Publication:

2024-09-09 19:00:05 UTC

Spatially varying and spatio-temporal dynamic linear models

Description

This package uses different hierarchical Bayesian spatio-temporal modelling strategies, namely:
(1) Spatially varying coefficient process models,
(2) Temporally varying coefficient process models, also known as the spatio-temporal dynamic linear models.

Details

Package:	spTDyn
Type:	Package

The back-end code of this package is built under c language.
Main functions used:
> GibbsDyn
> predict.spTD

Author(s)

K.S. Bakar
Maintainer: K.S. Bakar <shuvo.bakar@gmail.com>

References

Bakar, K. S., Kokic, P. and Jin, H. (2015). A spatio-dynamic model for assessing frost risk in south-eastern Australia. Journal of the Royal Statistical Society, Series C. DOI: 10.1111/rssc.12103
Bakar, K. S., Kokic, P. and Jin, H. (2015). Hierarchical spatially varying coefficient and temporal dynamic process models using spTDyn. Journal of Statistical Computation and Simulation. DOI:10.1080/00949655.2015.1038267

MCMC sampling for the models.

Description

This function is used to draw MCMC samples using the Gibbs sampler.

Usage

GibbsDyn(formula, data=parent.frame(), model="GP", time.data=NULL, coords, 
	priors=NULL, initials=NULL, nItr=5000, nBurn=1000, report=1, tol.dist=0.05, 
	distance.method="geodetic:km", cov.fnc="exponential", scale.transform="NONE", 
	spatial.decay=decay(distribution="FIXED"),truncation.para=list(at=0,lambda=2))

Arguments

formula

The symnbolic description of the model equation of the regression part of the space-time model. The terms sp and tp are used to define spatially and temporally varying parameters for the model.

data

An optional data frame containing the variables in the model. If omitted, the variables are taken from environment(formula), typically the environment from which spT.Gibbs is called. The data should be ordered first by the time and then by the sites specified by the coords below. One can also supply coordinates through this argument, where coordinate names should be "Latitude" and "Longitude".

model

The spatio-temporal models to be fitted, current choices are: "GP", and "truncated", with the first one as the default.

time.data

Defining the segments of the time-series set up using the function def.time.

coords

The n by 2 matrix or data frame defining the locations (e.g., longitude/easting, latitude/northing) of the fitting sites, where n is the number of fitting sites. One can also supply coordinates through a formula argument such as ~Longitude+Latitude.

priors

The prior distributions for the parameters. Default distributions are specified if these are not provided. If priors=NULL a flat prior distribution will be used with large variance. See details in priors.

initials

The preferred initial values for the parameters. If omitted, default values are provided automatically. Further details are provided in initials.

nItr

Number of MCMC iterations. Default value is 5000.

nBurn

Number of burn-in samples. This number of samples will be discarded before making any inference. Default value is 1000.

report

Number of reports to display while running the Gibbs sampler. Defaults to number of iterations.

distance.method

The preferred method to calculate the distance between any two locations. The available options are "geodetic:km", "geodetic:mile", "euclidean", "maximum", "manhattan", and "canberra". See details in dist. The default is "geodetic:km".

tol.dist

Minimum separation distance between any two locations out of those specified by coords, knots.coords and pred.coords. The default is 0.005. The programme will exit if the minimum distance is less than the non-zero specified value. This will ensure non-singularity of the covariance matrices.

cov.fnc

Covariance function for the spatial effects. The available options are "exponential", "gaussian", "spherical" and "matern". If "matern" is used then by default the smooth parameter (\nu) is estimated from (0,1) uniform distribution using discrete samples.

scale.transform

The transformation method for the response variable. Currently implemented options are: "NONE", "SQRT", and "LOG" with "NONE" as the deault.

spatial.decay

Provides the prior distribution for the spatial decay parameter \phi. Currently implemented options are "FIXED", "Unif", or "Gamm". Further details for each of these are specified by decay.

truncation.para

Provides truncation parameter \lambda and truncation point "at" using list.

Value

accept

The acceptance rate for the \phi parameter if the "MH" method of sampling is chosen.

phip

MCMC samples for the parameter \phi.

nup

MCMC samples for the parameter \nu. Only available if "matern" covariance function is used.

sig2eps

MCMC samples for the parameter \sigma^2_\epsilon.

sig2etap

MCMC samples for the parameter \sigma^2_\eta.

sig2betap

MCMC samples for the parameter \sigma^2_\beta, only applicable for spatially varying coefficient process model.

sig2deltap

MCMC samples for the parameter \sigma^2_\delta, for \beta_j, j=1,...,u. Only applicable for spatio-temporal DLM.

sig2op

MCMC samples for the parameter \sigma^2_o, for initial variance of \beta_0. Only applicable for spatio-dynamic and spatio-temporal DLM.

betap

MCMC samples for the parameter \beta.

rhop

MCMC samples for \rho.

op

MCMC samples for the true observations.

fitted

MCMC summary (mean and sd) for the fitted values.

tol.dist

Minimum tolerance distance limit between the locations.

distance.method

Name of the distance calculation method.

cov.fnc

Name of the covariance function used in model fitting.

scale.transform

Name of the scale.transformation method.

sampling.sp.decay

The method of sampling for the spatial decay parameter \phi.

covariate.names

Name of the covariates used in the model.

Distance.matrix

The distance matrix.

coords

The coordinate values.

n

Total number of sites.

r

Total number of segments in time, e.g., years.

T

Total points of time, e.g., days within each year.

p

Total number of model coefficients, i.e., \beta's including the intercept.

initials

The initial values used in the model.

priors

The prior distributions used in the model.

PMCC

The predictive model choice criteria obtained by minimising the expected value of a loss function, see Gelfand and Ghosh (1998). Results for both goodness of fit and penalty are given.

iterations

The number of samples for the MCMC chain, without burn-in.

nBurn

The number of burn-in period for the MCMC chain.

computation.time

The computation time required for the fitted model.

References

Bakar, K. S., Kokic, P. and Jin, H. (2015). A spatio-dynamic model for assessing frost risk in south-eastern Australia. Journal of the Royal Statistical Society, Series C. Bakar, K. S., Kokic, P. and Jin, H. (2015). Hierarchical spatially varying coefficient and temporal dynamic process models using spTDyn. Journal of Statistical Computation and Simulation.

Examples



##

###########################
## Attach library spTDyn
###########################

library(spTDyn)

## Read Aus data ##
data(AUSdata)
# set a side data for validation
library(spTimer)
s<-c(1,4,10)
AUSdataFit<-spT.subset(data=AUSdata, var.name=c("s.index"), s=s, reverse=TRUE)
AUSdataFit<-subset(AUSdataFit, with(AUSdataFit, !(year == 2009)))
AUSdataPred<-spT.subset(data=AUSdata, var.name=c("s.index"), s=s)
AUSdataPred<-subset(AUSdataPred, with(AUSdataPred, !(year == 2009)))
AUSdataFore<-spT.subset(data=AUSdata, var.name=c("s.index"), s=s)
AUSdataFore<-subset(AUSdataFore, with(AUSdataFore, (year == 2009)))

## Read NY data ##
data(NYdata)
# set a side data for validation
s<-c(5,8,10,15,20,22,24,26)
fday<-c(25:31)
NYdataFit<-spT.subset(data=NYdata, var.name=c("s.index"), s=s, reverse=TRUE)
NYdataFit<-subset(NYdataFit, with(NYdataFit, !(Day %in% fday & Month == 8)))
NYdataPred<-spT.subset(data=NYdata, var.name=c("s.index"), s=s)
NYdataPred<-subset(NYdataPred, with(NYdataPred, !(Day %in% fday & Month == 8)))
NYdataFore<-spT.subset(data=NYdata, var.name=c("s.index"), s=s)
NYdataFore<-subset(NYdataFore, with(NYdataFore, (Day %in% fday & Month == 8)))

## Code for analysing temperature data in Section: 4 ##
## Model: Spatially varying coefficient process models ##

nItr<-13000
nBurn<-3000

# MCMC via Gibbs using defaults
# Spatially varying coefficient process model

library("spTDyn", warn.conflicts = FALSE)
set.seed(11)
post.sp <- GibbsDyn(tmax ~ soi+sp(soi)+grid+sp(grid),
           data=AUSdataFit, nItr=nItr, nBurn=nBurn, coords=~lon+lat,
           spatial.decay=decay(distribution=Gamm(2,1),tuning=0.06))
print(post.sp)

## Table: 3, Section: 4.1 ##
post.sp$PMCC

# parameter summary
summary(post.sp) # without spatially varying coefficients
summary(post.sp, coefficient="spatial")

#plot(post.sp, density=FALSE)  # without spatially varying coefficients
#plot(post.sp, coefficient="spatial", density=FALSE)

## Code for Figures: 3(a), 3(b) Section: 4.1 ##
Figure_3a<-function(){
  boxplot(t(post.sp$betasp[1:9,]),pch=".",main="SOI",
          xlab="Sites",ylab="Values")
}
Figure_3b<-function(){
  boxplot(t(post.sp$betasp[10:18,]),pch=".",main="Grid",
          xlab="Sites",ylab="Values")
}
Figure_3a()
Figure_3b()

## spatial prediction
set.seed(11)
pred.sp <- predict(post.sp,newcoords=~lon+lat,newdata=AUSdataPred)

## Table: 4, Section: 4.1, validations ##
spT.validation(AUSdataPred$tmax,c(pred.sp$Mean))
plot(AUSdataPred$tmax,c(pred.sp$Mean))

## temporal prediction
set.seed(11)
pred.sp.f <- predict(post.sp,type="temporal",foreStep=12,
                     newcoords=~lon+lat, newdata=AUSdataFore)

## Table: 4, Section: 4.1, validations ##
spT.validation(AUSdataFore$tmax,c(pred.sp.f$Mean))
plot(AUSdataFore$tmax,c(pred.sp.f$Mean))

## Code for analysing Ozone data in Section: 4 ##
## Model: spatio-temporal DLM ##

# MCMC via Gibbs using defaults
# spatio-temporal DLM

library("spTDyn", warn.conflicts = FALSE)
set.seed(11)
post.tp <- GibbsDyn(o8hrmax ~ tp(cMAXTMP)-1, data=NYdataFit,
           nItr=nItr, nBurn=nBurn, coords=~Longitude+Latitude,
           initials=initials(rhotp=0), scale.transform="SQRT",
           spatial.decay=decay(distribution=Gamm(2,1),tuning=0.05))
print(post.tp)
summary(post.tp)

## Table: 5, Section: 4.2 ##
post.tp$PMCC

## Figure: 5, Section: 4.2 ##
Figure_5<-function(){
  stat<-apply(post.tp$betatp[1:55,],1,quantile,prob=c(0.025,0.5,0.975))
  plot(stat[2,],type="p",lty=3,col=1,ylim=c(min(c(stat)),max(c(stat))),
       pch=19,ylab="",xlab="Days",axes=FALSE,main="cMAXTMP",cex=0.8)
  for(i in 1:55){
    segments(i, stat[2,i], i, stat[3,i])
    segments(i, stat[2,i], i, stat[1,i])
  }
  axis(1,1:55,labels=1:55);axis(2)
  abline(v=31.5,lty=2)
  text(15,0.32,"July");  text(45,0.32,"August");
}
Figure_5()

## spatial prediction
set.seed(11)
pred.tp <- predict(post.tp, newdata=NYdataPred, newcoords=~Longitude+Latitude)

## Table 6, Section: 4.2, validation ##
spT.validation(NYdataPred$o8hrmax,c(pred.tp$Mean))

## temporal prediction
set.seed(11)
pred.tp.f <- predict(post.tp, newdata=NYdataFore, newcoords=~Longitude+Latitude,
                     type="temporal", foreStep=7)

## Table 6, Section: 4.2, validation ##
spT.validation(NYdataFore$o8hrmax,c(pred.tp.f$Mean))

######################################################
## The Truncated/Censored models:
######################################################

## Read Aus data ##
data(AUSdata)
# set the truncation point at tmax=30
AUSdata$tmax <- replace(AUSdata$tmax, AUSdata$tmax<=30, 30)

# set a side data for validation
library(spTimer)
s<-c(1,4,10)
AUSdataFit<-spT.subset(data=AUSdata, var.name=c("s.index"), s=s, reverse=TRUE)
AUSdataFit<-subset(AUSdataFit, with(AUSdataFit, !(year == 2009)))
AUSdataPred<-spT.subset(data=AUSdata, var.name=c("s.index"), s=s)
AUSdataPred<-subset(AUSdataPred, with(AUSdataPred, !(year == 2009)))
AUSdataFore<-spT.subset(data=AUSdata, var.name=c("s.index"), s=s)
AUSdataFore<-subset(AUSdataFore, with(AUSdataFore, (year == 2009)))

#
nItr <- 5000 # number of MCMC samples for each model
nBurn <- 1000 # number of burn-in from the MCMC samples
# Truncation at 30 
# fit truncated spatially varying model 

## The Truncated/Censored spatially varying models:
library("spTDyn", warn.conflicts = FALSE)
set.seed(11)
out <- GibbsDyn(tmax ~ soi+sp(soi)+grid+sp(grid),model="truncated",
           data=AUSdataFit, nItr=nItr, nBurn=nBurn, coords=~lon+lat,
           spatial.decay=decay(distribution=Gamm(2,1),tuning=0.06),
           truncation.para = list(at = 30,lambda = 2))
print(out)
summary(out)
head(fitted(out))
plot(out,density=FALSE)
#
head(cbind(AUSdataFit$tmax,fitted(out)[,1]))
plot(AUSdataFit$tmax,fitted(out)[,1])
spT.validation(AUSdataFit$tmax,fitted(out)[,1])

## spatial prediction
set.seed(11)
pred.sp <- predict(out,newcoords=~lon+lat,newdata=AUSdataPred)
spT.validation(AUSdataPred$tmax,c(pred.sp$Mean))
plot(AUSdataPred$tmax,c(pred.sp$Mean))

## temporal prediction
set.seed(11)
pred.sp.f <- predict(out,type="temporal",foreStep=12,
                     newcoords=~lon+lat, newdata=AUSdataFore)
spT.validation(AUSdataFore$tmax,c(pred.sp.f$Mean))
plot(AUSdataFore$tmax,c(pred.sp.f$Mean))

## The Truncated/Censored temporal dynamic DLM models:
library("spTDyn", warn.conflicts = FALSE)
set.seed(11)
out <- GibbsDyn(tmax ~ soi+tp(soi)+grid,model="truncated",
           data=AUSdataFit, nItr=nItr, nBurn=nBurn, coords=~lon+lat,
           spatial.decay=decay(distribution=Gamm(2,1),tuning=0.06),
           truncation.para = list(at = 30,lambda = 2))
print(out)
summary(out)
head(fitted(out))
plot(out,density=FALSE)
#
head(cbind(AUSdataFit$tmax,fitted(out)[,1]))
plot(AUSdataFit$tmax,fitted(out)[,1])
spT.validation(AUSdataFit$tmax,fitted(out)[,1])

## spatial prediction
set.seed(11)
pred.tp <- predict(out,newcoords=~lon+lat,newdata=AUSdataPred)
spT.validation(AUSdataPred$tmax,c(pred.tp$Mean))
plot(AUSdataPred$tmax,c(pred.tp$Mean))

## temporal prediction
set.seed(11)
pred.tp.f <- predict(out,type="temporal",foreStep=12,
                     newcoords=~lon+lat, newdata=AUSdataFore)
spT.validation(AUSdataFore$tmax,c(pred.tp.f$Mean))
plot(AUSdataFore$tmax,c(pred.tp.f$Mean))


##############################################################################

Combining observation and nearest grid locations and data.

Description

These commands combine observation and nearest grid locations, data.

Usage

ObsGridLoc(obsLoc, gridLoc, distance.method="geodetic:km", plot=FALSE)
gridTodata(gridData, gridLoc=NULL, gridLon=NULL, gridLat=NULL)
ObsGridData(obsData, gridData, obsLoc, gridLoc, distance.method="geodetic:km")

Arguments

obsLoc

The observed/measurement locations, first column is longitude/easting/x-axis and second column is latitude/northing/y-axis.

gridLoc

Grid locations, first column is longitude/easting/x-axis and second column is latitude/northing/y-axis.

distance.method

plot

Logical argument, if TRUE then plot observed and nearest grid locations.

gridData

Gridded data, should be in array form with dimenstions as longitude/x-axis, latitude/y-axis, day/time1, year/time2.

gridLon

Longitude/easting/x-axis of grid locations.

gridLat

Latitude/northing/y-axis of grid locations.

obsData

Observation data in data frame.

Examples

##

library(spTimer)
data(NYdata)	
data(NYgrid)

obsLoc<-unique(cbind(NYdata$Longitude,NYdata$Latitude))
gridLoc<-unique(cbind(NYgrid$Longitude,NYgrid$Latitude))

# find closest observed and grid locations
dat<-ObsGridLoc(obsLoc, gridLoc)
head(dat)
# with plots
dat<-ObsGridLoc(obsLoc, gridLoc, plot=TRUE)
head(dat)

# convert array gridData to spTimer data format
gridData<-array(1:(10*10*31*2),dim=c(10,10,31,2)) # lon, lat, day, year
dat<-gridTodata(gridData, gridLoc)
head(dat)

# combine observed and grid data and locations
obsData<-NYdata
gridData<-array(1:(10*10*31*2),dim=c(10,10,31,2)) # lon, lat, day, year
dat<-ObsGridData(obsData, gridData, obsLoc, gridLoc)
head(dat)

# combine observed and more than one grid datasets
obsData<-NYdata
gridData1<-array(1:(10*10*31*2),dim=c(10,10,31,2)) # lon, lat, day, year
gridData2<-array(((10*10*31*2)+1):(2*(10*10*31*2)),dim=c(10,10,31,2)) # lon, lat, day, year
gridLoc1<-unique(cbind(NYgrid$Longitude,NYgrid$Latitude))
gridLoc2<-unique(cbind(NYgrid$Longitude,NYgrid$Latitude))
dat<-ObsGridData(obsData, gridData=list(gridData1,gridData2),
        obsLoc, gridLoc=list(gridLoc1, gridLoc2))
head(dat)

##

Choice for sampling spatial decay parameter `\phi`.

Description

This function initialises the sampling method for the spatial decay parameter \phi.

Usage

decay(distribution=Gamm(a=2,b=1), tuning=NULL, npoints=NULL, value=NULL)

Arguments

distribution

Prior distribution for \phi. Currently available methods are, Gamm(a,b) and Unif(low,up). One can also used "FIXED" value for \phi parameter.

tuning

If the Gamma prior distribution is used then we need to define the tuning parameter for sampling \phi. The tuning is the standard deviation for the normal proposal distribution of the random-walk Metropolis algorithm used to sample \phi on the log-scale.

npoints

If Unif distribution is used then need to define the number of segments for the range of limits by npoints. Default value is 5.

value

If distribution="FIXED" type is used then need to define the value for \phi. The default value is 3/dmax where dmax is the maximum distance between the fitting sites provided by coords.

Examples

## 

# input for random-walk Metropolis within Gibbs 
# sampling for phi parameter
spatial.decay<-decay(distribution=Gamm(2,1), tuning=0.08)

# input for discrete sampling of phi parameter 
# with uniform prior distribution
spatial.decay<-decay(distribution=Unif(0.01,0.02),npoints=5)

# input for spatial decay if FIXED is used
spatial.decay<-decay(distribution="FIXED", value=0.01)

##

Timer series information.

Description

This function defines the time series in the spatio-temporal data.

Usage

def.time(t.series, segments=1)

Arguments

t.series

Number of times within each segment in each series. Can take only regular time-series.

segments

Number of segments in each time series. This should be a constant.

Examples

## 

# regular time-series in each year
time.data<-def.time(t.series=30,segments=2)

##

Initial values for the spatio-temporal models.

Description

This command is useful to assign the initial values of the hyper-parameters of the prior distributions.

Usage

initials(sig2eps=0.01, sig2eta=NULL, sig2beta=NULL, sig2delta=NULL,
   rhotp=NULL, rho=NULL, beta=NULL, phi=NULL)

Arguments

sig2eps

Initial value for the parameter \sigma^2_\epsilon.

sig2eta

Initial value for the parameter \sigma^2_\eta.

sig2beta

Initial value for the parameter \sigma^2_\beta for spatially varying model.

sig2delta

Initial value for the parameter \sigma^2_\delta for dynamic state-space model.

rhotp

Value for the parameter \rho for dynamic state-space model. For rhotp=1, \rho parameters are not sampled and fixed at value 1. For rhotp=0, \rho parameters are sampled from the full conditional distribution via MCMC with initial value 0.

rho

Initial value for the parameter \rho.

beta

Initial value for the parameter \beta.

phi

Initial value for the parameter \phi.

Note

Initial values are automatically given if the user does not provide these.

Examples

## 

initials<-initials(sig2eps=0.01, sig2eta=0.5, beta=NULL, phi=0.001)
initials

##

Plots for spTDyn output.

Description

This function is used to obtain MCMC summary, residual and fitted surface plots.

Usage

## S3 method for class 'spTD'
plot(x, residuals=FALSE, coefficient=NULL, ...)

##

Arguments

x

Object of class inheriting from "spTD".

residuals

If TRUE then plot residual vs. fitted and normal qqplot of the residuals. If FALSE then plot MCMC samples of the parameters using coda package. Defaults value is FALSE.

coefficient

Takes values: "spatial", "temporal" and "rho" for summary statistics of spatial, temporal and rho coefficients respectively. If NULL then provides parameter plots without spatial and temporal coefficients.

...

Other arguments.

Examples

## Not run: 
##

plot(out) # where out is the output from spT class
plot(out, residuals=TRUE) # where out is the output from spT class
plot(out, coefficient="spatial") # for spatially varying coefficients

##

## End(Not run)

Spatial and temporal predictions for the spatio-temporal models.

Description

This function is used to obtain spatial predictions in the unknown locations and also to get the temporal forecasts using MCMC samples.

Usage

## S3 method for class 'spTD'
predict(object, newdata, newcoords, foreStep=NULL, type="spatial", 
        nBurn, tol.dist, Summary=TRUE, ...)

Arguments

object

Object of class inheriting from "spTD".

newdata

The data set providing the covariate values for spatial prediction or temporal forecasts. This data should have the same space-time structure as the original data frame.

newcoords

The coordinates for the prediction or forecast sites. The locations are in similar format to coords, see spT.Gibbs.

foreStep

Number of K-step (time points) ahead forecast, K=1,2, ...; Only applicable if type="temporal".

type

If the value is "spatial" then only spatial prediction will be performed at the newcoords which must be different from the fitted sites provided by coords. When the "temporal" option is specified then forecasting will be performed and in this case the newcoords may also contain elements of the fitted sites in which case only temporal forecasting beyond the last fitted time point will be performed.

nBurn

Number of burn-in. Initial MCMC samples to discard before making inference.

tol.dist

Minimum tolerance distance limit between fitted and predicted locations.

Summary

To obtain summary statistics for the posterior predicted MCMC samples. Default is TRUE.

...

Other arguments.

Value

pred.samples or fore.samples

Prediction or forecast MCMC samples.

pred.coords or fore.coords

prediction or forecast coordinates.

Mean

Average of the MCMC predictions

Median

Median of the MCMC predictions

SD

Standard deviation of the MCMC predictions

Low

Lower limit for the 95 percent CI of the MCMC predictions

Up

Upper limit for the 95 percent CI of the MCMC predictions

computation.time

The computation time.

model

The model method used for prediction.

type

"spatial" or "temporal".

...

Other values "obsData", "fittedData" and "residuals" are provided only for temporal prediction.

References

Examples



##

library(spTDyn)

## Read Aus data ##
data(AUSdata)
# set a side data for validation
s<-c(1,4,10)
AUSdataFit<-spT.subset(data=AUSdata, var.name=c("s.index"), s=s, reverse=TRUE)
AUSdataFit<-subset(AUSdataFit, with(AUSdataFit, !(year == 2009)))
AUSdataPred<-spT.subset(data=AUSdata, var.name=c("s.index"), s=s)
AUSdataPred<-subset(AUSdataPred, with(AUSdataPred, !(year == 2009)))
AUSdataFore<-spT.subset(data=AUSdata, var.name=c("s.index"), s=s)
AUSdataFore<-subset(AUSdataFore, with(AUSdataFore, (year == 2009)))

## Read NY data ##
data(NYdata)
# set a side data for validation
s<-c(5,8,10,15,20,22,24,26)
fday<-c(25:31)
NYdataFit<-spT.subset(data=NYdata, var.name=c("s.index"), s=s, reverse=TRUE)
NYdataFit<-subset(NYdataFit, with(NYdataFit, !(Day %in% fday & Month == 8)))
NYdataPred<-spT.subset(data=NYdata, var.name=c("s.index"), s=s)
NYdataPred<-subset(NYdataPred, with(NYdataPred, !(Day %in% fday & Month == 8)))
NYdataFore<-spT.subset(data=NYdata, var.name=c("s.index"), s=s)
NYdataFore<-subset(NYdataFore, with(NYdataFore, (Day %in% fday & Month == 8)))

## Code for analysing temperature data in Section: 4 ##
## Model: Spatially varying coefficient process models ##

nItr<-13000
nBurn<-3000

# MCMC via Gibbs using defaults
# Spatially varying coefficient process model

library("spTDyn", warn.conflicts = FALSE)
set.seed(11)
post.sp <- GibbsDyn(tmax ~ soi+sp(soi)+grid+sp(grid),
           data=AUSdataFit, nItr=nItr, nBurn=nBurn, coords=~lon+lat,
           spatial.decay=decay(distribution=Gamm(2,1),tuning=0.06))
print(post.sp)

## Table: 3, Section: 4.1 ##
post.sp$PMCC

# parameter summary
summary(post.sp) # without spatially varying coefficients
summary(post.sp, coefficient="spatial")

#plot(post.sp, density=FALSE)  # without spatially varying coefficients
#plot(post.sp, coefficient="spatial", density=FALSE)

## Code for Figures: 3(a), 3(b) Section: 4.1 ##
Figure_3a<-function(){
  boxplot(t(post.sp$betasp[1:9,]),pch=".",main="SOI",
          xlab="Sites",ylab="Values")
}
Figure_3b<-function(){
  boxplot(t(post.sp$betasp[10:18,]),pch=".",main="Grid",
          xlab="Sites",ylab="Values")
}
Figure_3a()
Figure_3b()

## spatial prediction
set.seed(11)
pred.sp <- predict(post.sp,newcoords=~lon+lat,newdata=AUSdataPred)

## Table: 4, Section: 4.1, validations ##
spT.validation(AUSdataPred$tmax,c(pred.sp$Mean))
plot(AUSdataPred$tmax,c(pred.sp$Mean))

## temporal prediction
set.seed(11)
pred.sp.f <- predict(post.sp,type="temporal",foreStep=12,
                     newcoords=~lon+lat, newdata=AUSdataFore)

## Table: 4, Section: 4.1, validations ##
spT.validation(AUSdataFore$tmax,c(pred.sp.f$Mean))
plot(AUSdataFore$tmax,c(pred.sp.f$Mean))

## Code for analysing Ozone data in Section: 4 ##
## Model: spatio-temporal DLM ##

# MCMC via Gibbs using defaults
# spatio-temporal DLM

library("spTDyn", warn.conflicts = FALSE)
set.seed(11)
post.tp <- GibbsDyn(o8hrmax ~ tp(cMAXTMP)-1, data=NYdataFit,
           nItr=nItr, nBurn=nBurn, coords=~Longitude+Latitude,
           initials=initials(rhotp=0), scale.transform="SQRT",
           spatial.decay=decay(distribution=Gamm(2,1),tuning=0.05))
print(post.tp)
summary(post.tp)

## Table: 5, Section: 4.2 ##
post.tp$PMCC

## Figure: 5, Section: 4.2 ##
Figure_5<-function(){
  stat<-apply(post.tp$betatp[1:55,],1,quantile,prob=c(0.025,0.5,0.975))
  plot(stat[2,],type="p",lty=3,col=1,ylim=c(min(c(stat)),max(c(stat))),
       pch=19,ylab="",xlab="Days",axes=FALSE,main="cMAXTMP",cex=0.8)
  for(i in 1:55){
    segments(i, stat[2,i], i, stat[3,i])
    segments(i, stat[2,i], i, stat[1,i])
  }
  axis(1,1:55,labels=1:55);axis(2)
  abline(v=31.5,lty=2)
  text(15,0.32,"July");  text(45,0.32,"August");
}
Figure_5()

## spatial prediction
set.seed(11)
pred.tp <- predict(post.tp, newdata=NYdataPred, newcoords=~Longitude+Latitude)

## Table 6, Section: 4.2, validation ##
spT.validation(NYdataPred$o8hrmax,c(pred.tp$Mean))

## temporal prediction
set.seed(11)
pred.tp.f <- predict(post.tp, newdata=NYdataFore, newcoords=~Longitude+Latitude,
                     type="temporal", foreStep=7)

## Table 6, Section: 4.2, validation ##
spT.validation(NYdataFore$o8hrmax,c(pred.tp.f$Mean))

##############################################################################

Priors for the spatio-temporal models.

Description

This command is useful to assign the hyper-parameters of the prior distributions.

Usage

priors(inv.var.prior=Gamm(a=2,b=1),beta.prior=Norm(0,10^10), 
  rho.prior=Norm(0,10^10))

Arguments

inv.var.prior

The hyper-parameter for the Gamma prior distribution (with mean = a/b) of the precision (inverse variance) model parameters (e.g., 1/\sigma2_\epsilon, 1/\sigma2_\eta).

beta.prior

The hyper-parameter for the Normal prior distribution of the \beta model parameters.

rho.prior

The hyper-parameter for the Normal prior distribution of the \rho model parameter.

Note

If no prior information are given (assigned as NULL), then it use flat prior values of the corresponding distributions.
Gam and Nor refers to Gamma and Normal distributions respectively.

Examples

## 
library(spTimer)
priors<-priors(inv.var.prior=Gamm(2,1), beta.prior=Norm(0,10^4))
priors

##

Defining spatially varying coefficients in the formula

Description

This function is used to define spatially varying coefficients within the formula for the Gaussian process spatio-dynamic and spatially varying coefficient process models.

Usage

sp(x)

Arguments

x

The variable/covariate for which spatially varying coefficient is defined.

Examples



##

###########################
## Attach library spTimer
###########################

library(spTDyn)

###########################
## The GP models:
###########################

##
## Model fitting
##

# Read data 
data(NYdata); 

# Define the coordinates
coords<-as.matrix(unique(cbind(NYdata[,2:3])))

# MCMC via Gibbs using default choices
set.seed(11)
post.gp <- GibbsDyn(formula=o8hrmax ~cMAXTMP+WDSP+sp(RH),   
         data=NYdata, coords=coords, scale.transform="SQRT")
print(post.gp)

Service functions and some undocumented functions for the spTimer library

Description

Internal spTDyn functions

Summary statistics of the parameters.

Description

This function is used to obtain MCMC summary statistics.

Usage

## S3 method for class 'spTD'
summary(object, digits=4, package="spTDyn", coefficient=NULL, ...)

##

Arguments

object

Object of class inheriting from "spTD".

digits

Rounds the specified number of decimal places (default 4).

package

If "coda" then summary statistics are given using coda package. Defaults value is "spTDyn".

coefficient

Takes values: "spatial", "temporal" and "rho" for summary statistics of spatial, temporal and rho coefficients respectively. If NULL then provides parameter summary without spatial and temporal coefficients.

...

Other arguments.

Value

sig2eps

Summary statistics for \sigma_\epsilon^2.

sig2eta

Summary statistics for \sigma_\eta^2.

phi

Summary statistics for spatial decay parameter \phi, if estimated using decay.

...

Summary statistics for other parameters used in the models.

Examples

## Not run: 
##

summary(out) # where out is the output from spT class
summary(out, digit=2) # where out is the output from spT class
summary(out, pack="coda") # where out is the output from spT class
summary(out, coefficient="spatial") # for spatially varying coefficients
summary(out, coefficient="temporal") # for temporally varying coefficients

##

## End(Not run)

Defining dynamic time-series coefficients in the formula

Description

This function is used to define dynamic time-series coefficients within the formula for the Gaussian process spatio-dynamic and spatio-temporal DLM.

Usage

tp(x)

Arguments

x

The variable/covariate for which time varying coefficient is defined.

Examples



##

###########################
## Attach library spTimer
###########################

library(spTDyn)

###########################
## The GP models:
###########################

##
## Model fitting
##

# Read data 
data(NYdata); 

# Define the coordinates
coords<-as.matrix(unique(cbind(NYdata[,2:3])))

# MCMC via Gibbs using default choices
set.seed(11)
post.gp <- GibbsDyn(formula=o8hrmax ~cMAXTMP+WDSP+tp(RH),   
         data=NYdata, coords=coords, scale.transform="SQRT")
print(post.gp)

##

Spatially varying and spatio-temporal dynamic linear models

Description

Details

Author(s)

References

See Also

MCMC sampling for the models.

Description

Usage

Arguments

Value

References

See Also

Examples

Combining observation and nearest grid locations and data.

Description

Usage

Arguments

Examples

Choice for sampling spatial decay parameter \phi.

Description

Usage

Arguments

See Also

Examples

Timer series information.

Description

Usage

Arguments

See Also

Examples

Initial values for the spatio-temporal models.

Description

Usage

Arguments

Note

See Also

Examples

Plots for spTDyn output.

Description

Usage

Arguments

See Also

Examples

Spatial and temporal predictions for the spatio-temporal models.

Description

Usage

Arguments

Value

References

See Also

Examples

Priors for the spatio-temporal models.

Description

Usage

Arguments

Note

See Also

Examples

Defining spatially varying coefficients in the formula

Description

Usage

Arguments

See Also

Examples

Service functions and some undocumented functions for the spTimer library

Description

Summary statistics of the parameters.

Description

Usage

Arguments

Value

See Also

Examples

Defining dynamic time-series coefficients in the formula

Description

Usage

Arguments

See Also

Examples

Choice for sampling spatial decay parameter `\phi`.