SpatioTemporal: Spatio-Temporal Model Estimation

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Utilities that estimate, predict and cross-validate the spatio-temporal model developed for MESA Air.

Author
Johan Lindstrom, Adam Szpiro, Paul D. Sampson, Silas Bergen, Assaf P. Oron
Date of publication
2013-08-12 16:51:44
Maintainer
Johan Lindstrom <johanl@maths.lth.se>
License
GPL-2
Version
1.1.7

View on CRAN

Man pages

blockMult
Multiplication of Block Diagonal Matrix and Vector
boxplot.estCVSTmodel
Boxplots for 'estCVSTmodel' object
calc.FX
Compute Matrix Product Bewteen Temporal Trends and a LUR...
calc.FXtF2
Compute Quadratic Form Bewteen Temporal Trends and Sigma B
calc.mu.B
Matrix Multiplication with Block Matrices
calcSmoothTrends
Smooth Basis Functions for a STdata Object
calc.tFX
Compute Matrix Product Bewteen Temporal Trends and a Matrix
calc.tFXF
Compute Quadratic Form Bewteen Temporal Trends and Sigma nu
coef.estCVSTmodel
Returns estimated parameters for each CV-group.
coef.estimateSTmodel
Returns estimated parameters (and uncertaintes)
computeLTA
Computes the Long Term Average for Each Sites.
convertCharToDate
Convert Character to Dates
createCV
Define Cross-Validation Groups
createDataMatrix
Create a Data Matrix
createLUR
Add Covariate Fields to 'STdata' Object.
createSTdata
Construct STdata Object
createSTmodel
Construct STmodel Object
crossDist
Computed the Euclidian Distance Matrix
c.STmodel
Combine Several STmodel/STdata Objects
defaultList
Add Default Elements to Incomplete list
density.mcmcSTmodel
Kernel Density Estimation for an 'mcmcSTmodel' Object
detrendSTdata
Removes Temporal Trend from Observations in a 'STdata' Object
dotProd
Computes Inner Product and Squared 2-norm
dropObservations
Drop Observations from a STmodel
est.cv.mesa
Example of 'estCVSTmodel' and 'predCVSTmodel' structures
estimateBetaFields
Regression Estimates of beta-Fields
estimateCV.STmodel
Cross-Validated Estimation and Prediction
estimate.STmodel
Estimation of the Spatio-Temporal Model
est.mesa.model
Examples of 'estimateSTmodel' structure
evalCovFuns
Compute Covariance Function
expandF
Expand F
genGradient
Compute Finite Difference Gradient and Hessians.
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
loglikeSTnames
Create Names for Log-likelihood Parameters for STmodel...
makeCholBlock
Computations for Block Diagonal Matrices
make.sigma.B
Deprecated functions, use replacements!
makeSigmaB
Create Block Covariance Matrix (Equal Block Sizes)
makeSigmaNu
Create Block Covariance Matrix (Unequal Block Sizes)
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
namesCovFuns
Available covariance functions
parsCovFuns
Parameter Names for Covariance Function(s)
plot.density.mcmcSTmodel
Plots for an 'density.mcmcSTmodel' object
plot.mcmcSTmodel
Plots for an 'mcmcSTmodel' object
plot.predictSTmodel
Plots for 'predictSTmodel' and 'predCVSTmodel' Objects
plot.STdata
Different Plots for 'STdata'/'STmodel' object
plot.SVDcv
Plot and Boxplot cross-validation statistics for 'SVDcv'...
predictNaive
Naive Temporal Predictions
predict.STmodel
Computes Conditional Expectation at Unobserved Locations
pred.mesa.model
Example of a 'predictSTmodel' structure
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
processLocation
Internal Function that Extracts Locations
processLUR
Internal Function that do Covariate Selection
qqnorm.STdata
QQ-norm for 'STdata'/'STmodel'/'predCVSTmodel' objects
removeSTcovarMean
Mean-Centre the Spatio-Temporal Covariate
scatterPlot
Scatter plot
scatterPlot.STdata
scatterPlot for 'STdata'/'STmodel'/'predCVSTmodel' objects
simulate.STmodel
Simulate Data from the Spatio-Temporal Model
SpatioTemporal-package
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
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
SVDmiss
Missing Data SVD
SVDsmooth
Smooth Basis Functions for Data Matrix with Missing Values
updateCovf
Update Covariance Functions in 'STmodel' Objects
updateTrend.STdata
Update Trend in 'STdata' or 'STmodel' Object

Files in this package

SpatioTemporal
SpatioTemporal/inst
SpatioTemporal/inst/doc
SpatioTemporal/inst/doc/ST_tutorial.pdf
SpatioTemporal/inst/doc/ST_intro.Rnw
SpatioTemporal/inst/doc/ST_intro.pdf
SpatioTemporal/inst/doc/ST_tutorial.R
SpatioTemporal/inst/doc/ST_tutorial.Rnw
SpatioTemporal/inst/doc/ST_intro.R
SpatioTemporal/Rd_examples
SpatioTemporal/Rd_examples/Ex_mesa_model.R
SpatioTemporal/Rd_examples/Ex_makeSigmaB.R
SpatioTemporal/Rd_examples/Ex_calc_tFXF.R
SpatioTemporal/Rd_examples/Ex_calc_mu_B.R
SpatioTemporal/Rd_examples/Ex_detrendSTdata.R
SpatioTemporal/Rd_examples/Ex_dropObservations.R
SpatioTemporal/Rd_examples/Ex_estimate_STmodel.R
SpatioTemporal/Rd_examples/Ex_sumLogDiag.R
SpatioTemporal/Rd_examples/Ex_computeLTA.R
SpatioTemporal/Rd_examples/Ex_estimateBetaFields.R
SpatioTemporal/Rd_examples/Ex_createCV.R
SpatioTemporal/Rd_examples/Ex_estimateCV_STmodel.R
SpatioTemporal/Rd_examples/Ex_plot_mcmcSTmodel.R
SpatioTemporal/Rd_examples/Ex_blockMult.R
SpatioTemporal/Rd_examples/Ex_boxplot_estCVSTmodel.R
SpatioTemporal/Rd_examples/Ex_scatterPlot_STdata.R
SpatioTemporal/Rd_examples/Ex_qqnorm_STdata.R
SpatioTemporal/Rd_examples/Ex_MCMC_mesa_model.R
SpatioTemporal/Rd_examples/Ex_makeCholBlock.R
SpatioTemporal/Rd_examples/Ex_simulate_STmodel.R
SpatioTemporal/Rd_examples/Ex_c_STmodel.R
SpatioTemporal/Rd_examples/Ex_calc_FXtF2.R
SpatioTemporal/Rd_examples/Ex_predictNaive.R
SpatioTemporal/Rd_examples/Ex_processLocation.R
SpatioTemporal/Rd_examples/Ex_loglikeST.R
SpatioTemporal/Rd_examples/Ex_dotProd.R
SpatioTemporal/Rd_examples/Ex_evalCovFuns.R
SpatioTemporal/Rd_examples/Ex_SpatioTemporal_package.R
SpatioTemporal/Rd_examples/Ex_createSTdata.R
SpatioTemporal/Rd_examples/Ex_createDataMatrix.R
SpatioTemporal/Rd_examples/Ex_plot_predictSTmodel.R
SpatioTemporal/Rd_examples/Ex_expandF.R
SpatioTemporal/Rd_examples/Ex_calcSmoothTrends.R
SpatioTemporal/Rd_examples/Ex_loglikeSTGrad.R
SpatioTemporal/Rd_examples/Ex_updateCovf.R
SpatioTemporal/Rd_examples/Ex_mesa_data_raw.R
SpatioTemporal/Rd_examples/Ex_createSTmodel.R
SpatioTemporal/Rd_examples/Ex_density_mcmcSTmodel.R
SpatioTemporal/Rd_examples/Ex_makeSigmaNu.R
SpatioTemporal/Rd_examples/Ex_calc_tFX.R
SpatioTemporal/Rd_examples/Ex_convertCharToDate.R
SpatioTemporal/Rd_examples/Ex_loglikeSTgetPars.R
SpatioTemporal/Rd_examples/Ex_predict_STmodel.R
SpatioTemporal/Rd_examples/Ex_SVDsmooth.R
SpatioTemporal/Rd_examples/Ex_SVDmiss.R
SpatioTemporal/Rd_examples/Ex_plot_STdata.R
SpatioTemporal/Rd_examples/Ex_removeSTmean.R
SpatioTemporal/Rd_examples/Ex_crossDist.R
SpatioTemporal/Rd_examples/Ex_genGradient.R
SpatioTemporal/Rd_examples/Ex_processLUR.R
SpatioTemporal/Rd_examples/Ex_updateTrend.R
SpatioTemporal/Rd_examples/Ex_calc_FX.R
SpatioTemporal/src
SpatioTemporal/src/C_dist.c
SpatioTemporal/src/C_block_matrix_alg.c
SpatioTemporal/src/C_dotProd.c
SpatioTemporal/src/C_create_covariance.c
SpatioTemporal/src/C_sum_log_diag.c
SpatioTemporal/src/C_F_multiplications.c
SpatioTemporal/NAMESPACE
SpatioTemporal/data
SpatioTemporal/data/MCMC.mesa.model.RData
SpatioTemporal/data/mesa.data.raw.RData
SpatioTemporal/data/est.cv.mesa.RData
SpatioTemporal/data/pred.mesa.model.RData
SpatioTemporal/data/est.mesa.model.RData
SpatioTemporal/data/pred.cv.mesa.RData
SpatioTemporal/data/datalist
SpatioTemporal/data/mesa.model.RData
SpatioTemporal/R
SpatioTemporal/R/STmodel_simulate.R
SpatioTemporal/R/utils.R
SpatioTemporal/R/c_lin_alg.R
SpatioTemporal/R/MCMC.R
SpatioTemporal/R/loglikeST_aux.R
SpatioTemporal/R/STmodel.R
SpatioTemporal/R/CV_predict.R
SpatioTemporal/R/CV_aux.R
SpatioTemporal/R/STdata.R
SpatioTemporal/R/c_cov_matrices.R
SpatioTemporal/R/block_matrices.R
SpatioTemporal/R/temporal_SVD_incomplete_data.R
SpatioTemporal/R/loglikeST_derivatives.R
SpatioTemporal/R/loglikeST.R
SpatioTemporal/R/SpatioTemporal-data.R
SpatioTemporal/R/internal.R
SpatioTemporal/R/deprecated.R
SpatioTemporal/R/STmodel_setup.R
SpatioTemporal/R/STmodel_combine.R
SpatioTemporal/R/CV_estimate.R
SpatioTemporal/R/c_F_mult.R
SpatioTemporal/R/STmodel_processing.R
SpatioTemporal/R/STdata_processing.R
SpatioTemporal/R/STmodel_predict.R
SpatioTemporal/R/STmodel_estimate.R
SpatioTemporal/R/SpatioTemporal-package.R
SpatioTemporal/vignettes
SpatioTemporal/vignettes/tutorial.bib
SpatioTemporal/vignettes/ST_intro.Rnw
SpatioTemporal/vignettes/ST_tutorial.Rnw
SpatioTemporal/vignettes/vignette.sty
SpatioTemporal/MD5
SpatioTemporal/DESCRIPTION
SpatioTemporal/man
SpatioTemporal/man/print.estimateSTmodel.Rd
SpatioTemporal/man/plot.predictSTmodel.Rd
SpatioTemporal/man/dotProd.Rd
SpatioTemporal/man/print.summary.estCVSTmodel.Rd
SpatioTemporal/man/print.STdata.Rd
SpatioTemporal/man/parsCovFuns.Rd
SpatioTemporal/man/plot.SVDcv.Rd
SpatioTemporal/man/coef.estimateSTmodel.Rd
SpatioTemporal/man/print.STmodel.Rd
SpatioTemporal/man/crossDist.Rd
SpatioTemporal/man/processLocation.Rd
SpatioTemporal/man/loglikeSTnames.Rd
SpatioTemporal/man/loglikeST.Rd
SpatioTemporal/man/print.predCVSTmodel.Rd
SpatioTemporal/man/calc.FX.Rd
SpatioTemporal/man/MCMC.STmodel.Rd
SpatioTemporal/man/calc.tFXF.Rd
SpatioTemporal/man/plot.mcmcSTmodel.Rd
SpatioTemporal/man/SVDsmooth.Rd
SpatioTemporal/man/density.mcmcSTmodel.Rd
SpatioTemporal/man/make.sigma.B.Rd
SpatioTemporal/man/print.predictSTmodel.Rd
SpatioTemporal/man/defaultList.Rd
SpatioTemporal/man/loglikeSTdim.Rd
SpatioTemporal/man/estimate.STmodel.Rd
SpatioTemporal/man/summary.STdata.Rd
SpatioTemporal/man/summary.estCVSTmodel.Rd
SpatioTemporal/man/updateCovf.Rd
SpatioTemporal/man/stCheckFields.Rd
SpatioTemporal/man/createCV.Rd
SpatioTemporal/man/print.summary.predCVSTmodel.Rd
SpatioTemporal/man/calc.mu.B.Rd
SpatioTemporal/man/namesCovFuns.Rd
SpatioTemporal/man/calc.tFX.Rd
SpatioTemporal/man/createLUR.Rd
SpatioTemporal/man/detrendSTdata.Rd
SpatioTemporal/man/print.summary.mcmcSTmodel.Rd
SpatioTemporal/man/SVDmiss.Rd
SpatioTemporal/man/loglikeSTGrad.Rd
SpatioTemporal/man/predict.STmodel.Rd
SpatioTemporal/man/stCheckObs.Rd
SpatioTemporal/man/print.summary.STmodel.Rd
SpatioTemporal/man/genGradient.Rd
SpatioTemporal/man/stCheckClass.Rd
SpatioTemporal/man/plot.density.mcmcSTmodel.Rd
SpatioTemporal/man/scatterPlot.STdata.Rd
SpatioTemporal/man/makeSigmaB.Rd
SpatioTemporal/man/processLUR.Rd
SpatioTemporal/man/print.summary.STdata.Rd
SpatioTemporal/man/est.mesa.model.Rd
SpatioTemporal/man/loglikeSTgetPars.Rd
SpatioTemporal/man/pred.mesa.model.Rd
SpatioTemporal/man/predictNaive.Rd
SpatioTemporal/man/MCMC.mesa.model.Rd
SpatioTemporal/man/boxplot.estCVSTmodel.Rd
SpatioTemporal/man/blockMult.Rd
SpatioTemporal/man/createSTdata.Rd
SpatioTemporal/man/summary.predCVSTmodel.Rd
SpatioTemporal/man/calc.FXtF2.Rd
SpatioTemporal/man/evalCovFuns.Rd
SpatioTemporal/man/computeLTA.Rd
SpatioTemporal/man/summary.mcmcSTmodel.Rd
SpatioTemporal/man/makeSigmaNu.Rd
SpatioTemporal/man/print.estCVSTmodel.Rd
SpatioTemporal/man/SpatioTemporal-package.Rd
SpatioTemporal/man/createSTmodel.Rd
SpatioTemporal/man/updateTrend.STdata.Rd
SpatioTemporal/man/createDataMatrix.Rd
SpatioTemporal/man/print.mcmcSTmodel.Rd
SpatioTemporal/man/convertCharToDate.Rd
SpatioTemporal/man/print.SVDcv.Rd
SpatioTemporal/man/coef.estCVSTmodel.Rd
SpatioTemporal/man/c.STmodel.Rd
SpatioTemporal/man/mesa.model.Rd
SpatioTemporal/man/estimateBetaFields.Rd
SpatioTemporal/man/scatterPlot.Rd
SpatioTemporal/man/est.cv.mesa.Rd
SpatioTemporal/man/sumLogDiag.Rd
SpatioTemporal/man/summary.STmodel.Rd
SpatioTemporal/man/expandF.Rd
SpatioTemporal/man/estimateCV.STmodel.Rd
SpatioTemporal/man/makeCholBlock.Rd
SpatioTemporal/man/mesa.data.raw.Rd
SpatioTemporal/man/calcSmoothTrends.Rd
SpatioTemporal/man/stCheckSTcovars.Rd
SpatioTemporal/man/removeSTcovarMean.Rd
SpatioTemporal/man/dropObservations.Rd
SpatioTemporal/man/simulate.STmodel.Rd
SpatioTemporal/man/qqnorm.STdata.Rd
SpatioTemporal/man/plot.STdata.Rd
SpatioTemporal/man/stCheckCovars.Rd