Functional Geostatistics: Univariate and Multivariate Functional Spatial Prediction
The R package ‘SpatFD’ carries out functional kriging, cokriging, optimal sampling and simulation for spatial prediction of functional data. The framework of spatial prediction, optimal sampling and simulation are extended from scalar to functional data. ‘SpatFD’ is based on the Karhunen-Loève expansion that allows to represent the observed functions in terms of its empirical functional principal components. Based on this approach, the functional auto-covariances and cross-covariances required for spatial functional predictions and optimal sampling, are completely determined by the sum of the spatial auto-covariances and cross-covariances of the respective score components.
The package provides new classes of data and functions for modeling spatial dependence structure among curves. The spatial prediction of curves at unsampled locations can be carried out using two types of predictors, and both of them report, the respective variances of the prediction error. In addition, there is a function for the determination of spatial locations sampling configuration that ensures minimum variance of spatial functional prediction. There are also two functions for plotting predicted curves at each location and mapping the surface at each time point, respectively.
You can install the development version from Github.
install.packages("devtools")
devtools::install_github("mpbohorquezc/SpatFD-Functional-Geostatistics", ref = "main")The objects class and usage in the different functions are listed.
SpatFD return an object class ‘SpatFD’ which is used in
functional kriging and to obtain the spatial random field of
scores.KS_scores_lambdas,COKS_scores_lambdas
return an object class ‘KS_pred’,‘COKS_pred’ to use in the linear
combinations to obtain functional kriging and cokriging. Plots are made
with ggplot_KS and ggmap_KS.FD_optimal_design return an object class
‘OptimalSpatialDesign’ that can be used with print.library(SpatFD)
library(gstat)
# Load data and coordinates
data(AirQualityBogota)
#s_0 nonsampled location. It could be data.frame or matrix and one or more locations of interest
newcoorden=data.frame(X=seq(93000,105000,len=100),Y=seq(97000,112000,len=100))
#newcoorden=data.frame(X=110000,Y=126000)
#newcoorden=matrix(c(110000.23,109000,109500,130000.81,129000,131000),nrow=3,ncol=2,byrow=T)
# Building the SpatFD object
SFD_PM10 <- SpatFD(PM10, coords = coord[, -1], basis = "Bsplines", nbasis = 17,norder=5, lambda = 0.00002, nharm=3)
summary(SFD_PM10)
# Semivariogram models for each spatial random field of scores
modelos <- list(vgm(psill = 2199288.58, "Wav", range = 1484.57, nugget = 0),
vgm(psill = 62640.74, "Mat", range = 1979.43, nugget = 0,kappa=0.68),
vgm(psill =37098.25, "Exp", range = 6433.16, nugget = 0))
# Functional kriging. Functional spatial prediction at each location of interest
#method = "lambda"
#Computation of lambda_i
KS_SFD_PM10_l <- KS_scores_lambdas(SFD_PM10, newcoorden ,method = "lambda", model = modelos)
class(KS_SFD_PM10_l)
# method = "scores"
#Simple kriging of scores
KS_SFD_PM10_sc <- KS_scores_lambdas(SFD_PM10, newcoorden, method = "scores", model = modelos)
# method = "both"
KS_SFD_PM10_both <- KS_scores_lambdas(SFD_PM10, newcoorden, method = "both", model = modelos)
summary(KS_SFD_PM10_l)
summary(KS_SFD_PM10_sc)
summary(KS_SFD_PM10_both)
# Linear combinations among weigths predictions and eigenfunctions
recons_fd(KS_SFD_PM10_l)
recons_fd(KS_SFD_PM10_sc)
recons_fd(KS_SFD_PM10_both)
# Curve and variance prediction plots
ggplot_KS(KS_SFD_PM10_l)
ggplot_KS(KS_SFD_PM10_l, show.varpred = T)
ggplot_KS(KS_SFD_PM10_sc)
ggplot_KS(KS_SFD_PM10_sc, show.varpred = T)
#Curve and variance prediction for both methods
PlotKS=ggplot_KS(KS_SFD_PM10_both,
main = "Plot 1 - Using Scores",
main2 = "Plot 2 - Using Lambda",
ylab = "PM10")
PlotKS[[1]]
PlotKS[[2]]
# Smoothed prediction maps for the given specific times
ggmap_KS(KS_SFD_PM10_l,
map_path = map,
window_time = c(3500),
zmin = 25,
zmax = 100)
ggmap_KS(KS_SFD_PM10_both,
map_path = map,
window_time = c(2108),
method = "lambda",
zmin = 50,
zmax = 120)
ggmap_KS(KS_SFD_PM10_both,
map_path = map,
window_time = c(5108,5109,5110),
method = "scores",
zmin = 50,
zmax = 120)
# Cross Validation
crossval_loo(KS_SFD_PM10_l)
crossval_loo(KS_SFD_PM10_sc)
crossval_loo(KS_SFD_PM10_both)
# Optimal spatial design
s0 <- cbind(2*runif(100),runif(100)) # random coordinates on (0,2)x(0,1)
fixed_stations <- cbind(2*runif(4),runif(4))
x_grid <- seq(0,2,length = 30)
y_grid <- seq(0,1,length = 30)
grid <- cbind(rep(x_grid,each = 30),rep(y_grid,30))
model <- vgm(psill = 5.665312,
model = "Exc",
range = 8000,
kappa = 1.62,
add.to = vgm(psill = 0.893,
model = "Nug",
range = 0,
kappa = 0))
FD_optimal_design(k = 10, s0 = s0, model = model,
grid = grid, nharm = 2, plt = TRUE,
fixed_stations = fixed_stations) -> OSD
OSD$new_stations
OSD$fixed_stations
OSD$plot
class(OSD)
#### Real Data Example ####
vgm_model <- vgm(psill = 5.665312,
model = "Exc",
range = 8000,
kappa = 1.62,
add.to = vgm(psill = 0.893,
model = "Nug",
range = 0,
kappa = 0))
my.CRS <- sp::CRS("EPSG:21899") # https://epsg.io/21899
map <- as(map, "Spatial")
bogota_shp <- sp::spTransform(map,my.CRS)
target <- sp::spsample(bogota_shp,n = 100, type = "random")
# The set of points in which we want to predict optimally.
old_stations <- sp::spsample(bogota_shp,n = 3, type = "random")
# The set of stations that are already fixed.
FD_optimal_design(k = 10, s0 = target,model = vgm_model,
map = map,plt = TRUE,
fixed_stations = old_stations) -> res
res
class(res)
# Functional cokriging
data(COKMexico)
SFD_PM10_NO2 <- SpatFD(Mex_PM10, coords = coord_PM10, basis = "Fourier", nbasis = 21, lambda = 0.000001, nharm = 2)
SFD_PM10_NO2 <- SpatFD(NO2, coords = coord_NO2, basis = "Fourier", nbasis = 27, lambda = 0.000001, nharm = 2,
add = SFD_PM10_NO2)
model1 <- gstat::vgm(647677.1,"Gau",23317.05)
model1 <- gstat::vgm(127633,"Wav",9408.63, add.to = model1)
newcoords <- data.frame(x = 509926,y = 2179149)
COKS_Mex <- COKS_scores_lambdas(SFD_PM10_NO2,newcoords,model1)
summary(COKS_Mex)
ggplot_KS(COKS_Mex)
ggmap_KS(COKS_Mex,map_path = map_mex,method = 'scores')You can read:
This package is free and open source software, licensed under GPL-3.