pred.strk: Spatio-temporal regression kriging prediction

In meteo: RFSI and Spatio-Temporal Geostatistical Interpolation for Meteorological and Other Environmental Variables

Spatio-temporal regression kriging prediction

Description

Function for spatio-temporal regression kriging prediction based on krigeST.

Usage

pred.strk(data,
          obs.col=1,
          data.staid.x.y.z = NULL,
          newdata,
          newdata.staid.x.y.z = NULL,
          z.value = NULL,
          crs = NA,
          zero.tol=0,
          reg.coef,
          vgm.model,
          sp.nmax=20,
          time.nmax=2,
          by='time',
          tiling= FALSE,
          ntiles=64,
          output.format = "STFDF",
          parallel.processing = FALSE,
          pp.type = "snowfall",
          cpus=detectCores()-1,
          computeVar=FALSE,
          progress=TRUE,
          ...)

Arguments

data	STFDF-class, STSDF-class, STIDF-class, sf-class, sftime-class, SpatVector-class or data.frame; Contains target variable (observations) and covariates in space and time used to perform STRK. If data.frame object, it should have next columns: station ID (staid), longitude (x), latitude (y), 3rd component - time, depth, ... (z) of the observation, observation value (obs), and covariates (cov1, cov2, ...). Covariate names should be the same as in the reg.coef (see below). If covariates are missing, overlay with newdata is tried. If overlay with newdata is not possible, then spatio-temporal ordinary kriging is performed.
obs.col	numeric or character; Column name or number showing position of the observation column in the data. Default is 1.
data.staid.x.y.z	numeric or character vector; Positions or names of the station ID (staid), longitude (x), latitude (y) and 3rd component - time, depth (z) columns in data.frame object (e.g. c(1,2,3,4)). If data is sf-class, sftime-class, or SpatVector-class object, data.staid.x.y.z is used to point staid and z position. Default is NULL.
newdata	STFDF-class, STSDF-class, STIDF-class, sf-class, sftime-class, SpatVector-class, SpatRaster-class or data.frame; Contains prediction locations and covariates used for STRK prediction. If data.frame object, it should have next columns: prediction location ID (staid), longitude (x), latitude (y), 3rd component - time, depth, ... (z), and covariates (cov1, cov2, ...). Covariate names have to be the same as in the reg.coef (see below).
newdata.staid.x.y.z	numeric or character vector; Positions or names of the prediction location ID (staid), longitude (x), latitude (y) and 3rd component (z) columns in data.frame newdata object (e.g. c(1,2,3,4)). If newdata is sf-class, sftime-class, SpatVector-class or SpatRaster-class object, newdata.staid.x.y.z is used to point staid and z position. Default is NULL.
z.value	vector; A vector of 3rd component - time, depth, ... (z) values if newdata is SpatRaster-class.
crs	st_crs or crs; Source CRS of data and newdata. If data or newdata contains crs, crs will not be used. Default is NA.
zero.tol	numeric; A distance value below (or equal to) which locations are considered as duplicates. Default is 0. See rm.dupl. Duplicates are removed to avoid singular covariance matrices in kriging.
reg.coef	numeric; Vector of named linear regression coefficients. Names of the coefficients (e.g. "Intercept", "temp_geo", "modis", "dem", "twi") will be used to match appropriate covariates from data. Coefficients for metorological variables (temperature, precipitation, etc.) can be taken from data(tregcoef) or can be specified by the user.
vgm.model	StVariogramModel list; Spatio-temporal variogram of regression residuals (or observations if spatio-temporal ordinary kriging). See vgmST. Spatio-temporal variogram model on residuals for metorological variables (temperature, precipitation, etc.) can be taken from data(tvgms) or can be specified by the user as a vgmST object.
sp.nmax	numeric; A number of spatially nearest observations that should be used for kriging predictions. If tiling is TRUE (see below), then is a number of spatially nearest observations that should be used for each tile. Deafult is 20.
time.nmax	numeric; A number of temporally nearest observations that should be used for kriging predictions Deafult is 2.
by	cahracter; Will foreach loop by time (default) or station. If station is set, sp.nmax will be used for each station prediction.
tiling	logical; Should simplified local kriging be used. Default is FALSE. If TRUE, area is divided in tiles and kriging calculation is done for each tile separately. Number of observation used per tile is defined with sp.nmax and time.nmax. If FALSE, temporal local kriging will be applied defined.
ntiles	numeric; A number of tiles for tilling. Default is 64. Ideally, each tile should contain less observations than sp.nmax and observations fall in neighboring tiles.
output.format	character; Format of the output, STFDF-class (default), STSDF-class, STIDF-class, data.frame, sf-class, sftime-class, SpatVector-class, or SpatRaster-class.
parallel.processing	logical; If parallel processing is performed. Default is FALSE.
pp.type	character; Type (R package) for parallel processing, "snowfall" (default) or "doParallel".
cpus	numeric; Number of processing units. Default is detectCores()-1.
computeVar	logical; If kriging variance is computed. Default is FALSE.
progress	logical; If progress bar is shown. Default is TRUE.
...	Further arguments passed to krigeST function.

Value

A STFDF-class, STSDF-class, STIDF-class, data.frame, sf-class, sftime-class, SpatVector-class, or SpatRaster-class object (depends on output.format argument), with columns (elements):

pred	Predictions.
tlm	Trend.
var	Kriging variance, if computeVar=TRUE.

Author(s)

Milan Kilibarda [e-mail], Aleksandar Sekulic [e-mail]

References

Kilibarda, M., T. Hengl, G. B. M. Heuvelink, B. Graeler, E. Pebesma, M. Percec Tadic, and B. Bajat (2014), Spatio-temporal interpolation of daily temperatures for global land areas at 1 km resolution, J. Geophys. Res. Atmos., 119, 2294-2313, doi:10.1002/2013JD020803.

See Also

tregcoef tvgms regdata meteo2STFDF tgeom2STFDF

Examples

library(sp)
library(spacetime)
library(sf)
library(gstat)
library(plyr)
# prepare data
# load observation - data.frame of mean temperatures
# preparing data
data(dtempc) 
data(stations)
data(regdata) # covariates, made by mete2STFDF function
regdata@sp@proj4string <- CRS('+proj=longlat +datum=WGS84')

lonmin=18 ;lonmax=22.5 ; latmin=40 ;latmax=46
serbia = point.in.polygon(stations$lon, stations$lat, c(lonmin,lonmax,lonmax,lonmin), 
                          c(latmin,latmin,latmax,latmax))
st = stations[ serbia!=0, ] # stations in Serbia approx.
obs.staid.time = c("staid", "time")
stations.staid.lon.lat = c(1,2,3)
crs = CRS('+proj=longlat +datum=WGS84')
delta = NULL

## Not run: 
# create STFDF
stfdf <- meteo2STFDF(obs = dtempc,
                     stations = st,
                     crs = crs)

# Calculate prediction of mean temperatures for "2011-07-05" and "2011-07-06" 
# global model is used for regression and variogram
# load precalculated variograms
data(tvgms) # ST variogram models
data(tregcoef) # MLR coefficients

### Example with STFDF and without parallel processing
results <- pred.strk(data = stfdf, # observations
                     newdata = regdata, # prediction locations with covariates
                     # newdata = regdata[,2,drop=FALSE], # for one day only
                     output.format = "STFDF", # data.frame | sf | sftime | SpatVector | SpatRaster 
                     reg.coef = tregcoef[[1]], # MLR coefficients
                     vgm.model = tvgms[[1]], # STRK variogram model
                     sp.nmax = 20,
                     time.nmax = 2,
                     computeVar=TRUE
)
class(results)
# plot prediction
# results@sp=as(results@sp,'SpatialPixelsDataFrame')
# stplot(results[,,"pred", drop= FALSE], col.regions=bpy.colors())
# stplot(results[,,"var", drop= FALSE], col.regions=bpy.colors())

## End(Not run)

## Not run: 
### Example with data.frames and parallel processing - SpatRaster output
library(terra)
library(doParallel)
# create data.frame
stfdf.df <- join(dtempc, st)
summary(stfdf.df)
regdata.df <- as.data.frame(regdata)
results <- pred.strk(data = stfdf.df,
                     obs.col = 3,
                     data.staid.x.y.z = c(1,4,5,2),
                     newdata = regdata.df,
                     newdata.staid.x.y.z = c(3,1,2,4),
                     crs = CRS("EPSG:4326"),
                     output.format = "SpatRaster", # STFDF |data.frame | sf | sftime | SpatVector
                     reg.coef = tregcoef[[1]],
                     vgm.model = tvgms[[1]],
                     sp.nmax = 20,
                     time.nmax = 2,
                     parallel.processing = TRUE,
                     pp.type = "doParallel", # "snowfall"
                     cpus = 1, # detectCores()-1,
                     computeVar = TRUE,
                     progress = TRUE
)
# plot prediction
# plot(results$`2011-07-06`[["pred"]])
# plot(results$`2011-07-06`[["var"]])

## End(Not run)

meteo documentation built on Oct. 14, 2023, 5:07 p.m.