# Spatio-Temporal Model Estimation

## Documentation for package ‘SpatioTemporal’ version 1.1.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

B C D E F G I L M N P Q R S T U

SpatioTemporal-package | Spatio-Temporal Modelling

## -- B --

block.mult | Deprecated functions, use replacements!
blockMult | Multiplication of Block Diagonal Matrix and Vector
boxplot.estCVSTmodel | Boxplots for 'estCVSTmodel' object
boxplot.SVDcv | Plot and Boxplot cross-validation statistics for 'SVDcv' object

## -- C --

c.STmodel | Combine Several STmodel/STdata Objects
calc.F.times.X | Deprecated functions, use replacements!
calc.FX | Compute Matrix Product Bewteen Temporal Trends and a LUR components
calc.FXtF2 | Compute Quadratic Form Bewteen Temporal Trends and Sigma B
calc.iS.X | Matrix Multiplication with Block Matrices
calc.mu.B | Matrix Multiplication with Block Matrices
calc.smooth.trends | Deprecated functions, use replacements!
calc.tF.mat.F | Deprecated functions, use replacements!
calc.tF.times.mat | Deprecated functions, use replacements!
calc.tFX | Compute Matrix Product Bewteen Temporal Trends and a Matrix
calc.tFXF | Compute Quadratic Form Bewteen Temporal Trends and Sigma nu
calc.X.iS.X | Matrix Multiplication with Block Matrices
calcSmoothTrends | Smooth Basis Functions for a STdata Object
coef.estCVSTmodel | Returns estimated parameters for each CV-group.
coef.estimateSTmodel | Returns estimated parameters (and uncertaintes)
combineMesaData | Deprecated functions, use replacements!
compute.ltaCV | Deprecated functions, use replacements!
computeLTA | Computes the Long Term Average for Each Sites.
cond.expectation | Deprecated functions, use replacements!
construct.LUR.basis | Deprecated functions, use replacements!
construct.ST.basis | Deprecated functions, use replacements!
convertCharToDate | Convert Character to Dates
create.data.matrix | Deprecated functions, use replacements!
create.data.model | Deprecated functions, use replacements!
createCV | Define Cross-Validation Groups
createDataMatrix | Create a Data Matrix
createLUR | Add Covariate Fields to 'STdata' Object.
createST | Add Covariate Fields to 'STdata' Object.
createSTdata | Construct STdata Object
createSTmodel | Construct STmodel Object
crossDist | Computed the Euclidian Distance Matrix
CVbasics | Deprecated functions, use replacements!
CVresiduals.qqnorm | Deprecated functions, use replacements!
CVresiduals.scatter | Deprecated functions, use replacements!

## -- D --

default.LUR.list | Deprecated functions, use replacements!
default.ST.list | Deprecated functions, use replacements!
defaultList | Add Default Elements to Incomplete list
density.mcmcSTmodel | Kernel Density Estimation for an 'mcmcSTmodel' Object
detrend.data | Deprecated functions, use replacements!
detrendSTdata | Removes Temporal Trend from Observations in a 'STdata' Object
dot.prod | Deprecated functions, use replacements!
dotProd | Computes Inner Product and Squared 2-norm
drop.observations | Deprecated functions, use replacements!
dropObservations | Drop Observations from a STmodel

## -- E --

est.cv.mesa | Example of 'estCVSTmodel' and 'predCVSTmodel' structures
est.mesa.model | Examples of 'estimateSTmodel' structure
estimate | Estimation of the Spatio-Temporal Model
estimate.STmodel | Estimation of the Spatio-Temporal Model
estimateBetaFields | Regression Estimates of beta-Fields
estimateCV | Cross-Validated Estimation and Prediction
estimateCV.STmodel | Cross-Validated Estimation and Prediction
evalCovFuns | Compute Covariance Function
expandF | Expand F

## -- F --

fit.mesa.model | Deprecated functions, use replacements!

## -- G --

gen.gradient | Deprecated functions, use replacements!
gen.hessian | Deprecated functions, use replacements!
genGradient | Compute Finite Difference Gradient and Hessians.
genHessian | Compute Finite Difference Gradient and Hessians.
get.params | Deprecated functions, use replacements!

## -- I --

invCholBlock | Computations for Block Diagonal Matrices

## -- L --

loglike | Deprecated functions, use replacements!
loglike.dim | Deprecated functions, use replacements!
loglike.grad | Deprecated functions, use replacements!
loglike.hessian | Deprecated functions, use replacements!
loglike.naive | Deprecated functions, use replacements!
loglike.naive.grad | Deprecated functions, use replacements!
loglike.naive.hessian | Deprecated functions, use replacements!
loglike.var.names | Deprecated functions, use replacements!
loglikeST | Compute the Log-likelihood for the Spatio-Temporal Model
loglikeSTdim | Dimensions of the STmodel Structure
loglikeSTgetPars | Extract Parameters from a Vector
loglikeSTGrad | Compute Gradient and Hessian for the Log-likelihood
loglikeSTHessian | Compute Gradient and Hessian for the Log-likelihood
loglikeSTnaive | Compute the Log-likelihood for the Spatio-Temporal Model
loglikeSTnaiveGrad | Compute Gradient and Hessian for the Log-likelihood
loglikeSTnaiveHessian | Compute Gradient and Hessian for the Log-likelihood
loglikeSTnames | Create Names for Log-likelihood Parameters for STmodel objects

## -- M --

make.sigma.B | Deprecated functions, use replacements!
make.sigma.B.full | Deprecated functions, use replacements!
make.sigma.nu | Deprecated functions, use replacements!
make.sigma.nu.cross.cov | Deprecated functions, use replacements!
makeCholBlock | Computations for Block Diagonal Matrices
makeSigmaB | Create Block Covariance Matrix (Equal Block Sizes)
makeSigmaNu | Create Block Covariance Matrix (Unequal Block Sizes)
MCMC | MCMC Inference of Parameters in the Spatio-Temporal Model
MCMC.mesa.model | Example of a 'mcmcSTmodel' structure
MCMC.STmodel | MCMC Inference of Parameters in the Spatio-Temporal Model
mesa.data.raw | Data used in the examples
mesa.model | Example of a 'STmodel' structure

## -- N --

namesCovFuns | Available covariance functions
norm2 | Computes Inner Product and Squared 2-norm

## -- P --

parsCovFuns | Parameter Names for Covariance Function(s)
plot.density.mcmcSTmodel | Plots for an 'density.mcmcSTmodel' object
plot.mcmcSTmodel | Plots for an 'mcmcSTmodel' object
plot.predCVSTmodel | Plots for 'predictSTmodel' and 'predCVSTmodel' Objects
plot.predictSTmodel | Plots for 'predictSTmodel' and 'predCVSTmodel' Objects
plot.STdata | Different Plots for 'STdata'/'STmodel' object
plot.STmodel | Different Plots for 'STdata'/'STmodel' object
plot.SVDcv | Plot and Boxplot cross-validation statistics for 'SVDcv' object
plotCV | Deprecated functions, use replacements!
plotMesaData | Deprecated functions, use replacements!
plotMonitoringLoc | Deprecated functions, use replacements!
plotPrediction | Deprecated functions, use replacements!
pred.cv.mesa | Example of 'estCVSTmodel' and 'predCVSTmodel' structures
pred.mesa.model | Example of a 'predictSTmodel' structure
predict.STmodel | Computes Conditional Expectation at Unobserved Locations
predictCV | Cross-Validated Estimation and Prediction
predictCV.STmodel | Cross-Validated Estimation and Prediction
predictNaive | Naive Temporal Predictions
print.estCVSTmodel | Print details for 'estCVSTmodel' object
print.estimateSTmodel | Print details for 'estimateSTmodel' object
print.mcmcSTmodel | Print details for 'mcmcSTmodel' object
print.predCVSTmodel | Print details for 'predCVSTmodel' object
print.predictSTmodel | Print details for 'predictSTmodel' object
print.STdata | Print details for 'STdata' object
print.STmodel | Print details for 'STmodel' object
print.summary.estCVSTmodel | Print details for 'summary.estCVSTmodel' object
print.summary.mcmcSTmodel | Print details for 'summary.mcmcSTmodel' object
print.summary.predCVSTmodel | Print details for 'summary.predCVSTmodel' object
print.summary.STdata | Print details for 'summary.STdata' object
print.summary.STmodel | Print details for 'summary.STmodel' object
print.SVDcv | Print details for 'SVDcv' object
printMesaDataNbrObs | Deprecated functions, use replacements!
processLocation | Internal Function that Extracts Locations
processLUR | Internal Function that do Covariate Selection
processST | Internal Function that do Covariate Selection

## -- Q --

qqnorm.predCVSTmodel | QQ-norm for 'STdata'/'STmodel'/'predCVSTmodel' objects
qqnorm.STdata | QQ-norm for 'STdata'/'STmodel'/'predCVSTmodel' objects
qqnorm.STmodel | QQ-norm for 'STdata'/'STmodel'/'predCVSTmodel' objects

## -- R --

remove.ST.mean | Deprecated functions, use replacements!
removeSTcovarMean | Mean-Centre the Spatio-Temporal Covariate
run.MCMC | Deprecated functions, use replacements!

## -- S --

scatterPlot | Scatter plot
scatterPlot.predCVSTmodel | scatterPlot for 'STdata'/'STmodel'/'predCVSTmodel' objects
scatterPlot.STdata | scatterPlot for 'STdata'/'STmodel'/'predCVSTmodel' objects
scatterPlot.STmodel | scatterPlot for 'STdata'/'STmodel'/'predCVSTmodel' objects
setupSTdataset | Deprecated functions, use replacements!
simulate.STmodel | Simulate Data from the Spatio-Temporal Model
simulateMesaData | Deprecated functions, use replacements!
solveTriBlock | Computations for Block Diagonal Matrices
SpatioTemporal | Spatio-Temporal Modelling
stCheckClass | Test if an object belongs to given class(es).
stCheckCovars | Check a data.frame of Covariates
stCheckFields | Test if fields exist in an object.
stCheckObs | Check an 'obs' data.frame.
stCheckSTcovars | Check an Array/List of Spatio-Temporal Covariates
sumLog | Sum the Logarithm of (Diagonal) Elements
sumLogDiag | Sum the Logarithm of (Diagonal) Elements
summary.estCVSTmodel | Computes summary details for 'estCVSTmodel' object
summary.mcmcSTmodel | Computes summary details for 'mcmcSTmodel' object
summary.predCVSTmodel | Computes summary details for 'predCVSTmodel' object
summary.STdata | Computes summary details for 'STdata' object
summary.STmodel | Computes summary details for 'STmodel' object
summary.SVDcv | Print details for 'SVDcv' object
summaryStatsCV | Deprecated functions, use replacements!
SVD.miss | Deprecated functions, use replacements!
SVD.smooth | Deprecated functions, use replacements!
SVD.smooth.cv | Deprecated functions, use replacements!
SVDmiss | Missing Data SVD
SVDsmooth | Smooth Basis Functions for Data Matrix with Missing Values
SVDsmoothCV | Smooth Basis Functions for Data Matrix with Missing Values

## -- T --

tstat | Deprecated functions, use replacements!

## -- U --

updateCovf | Update Covariance Functions in 'STmodel' Objects
updateSTdataTrend | Update Trend in 'STdata' or 'STmodel' Object
updateTrend | Update Trend in 'STdata' or 'STmodel' Object
updateTrend.STdata | Update Trend in 'STdata' or 'STmodel' Object
updateTrend.STmodel | Update Trend in 'STdata' or 'STmodel' Object