SpatioTemporal: Spatio-Temporal Model Estimation

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

AuthorJohan Lindstrom, Adam Szpiro, Paul D. Sampson, Silas Bergen, Assaf P. Oron
Date of publication2013-08-12 16:51:44
MaintainerJohan Lindstrom <johanl@maths.lth.se>
LicenseGPL-2
Version1.1.7

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

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