R

Performs an automatic interpolation

calsalmon April 21, 2014
autoKrige R Documentation

Performs an automatic interpolation

Description

This function performs automatic kriging on the given dataset. The variogram is generated automatically using autofitVariogram.

Usage

autoKrige(formula, 
  	  input_data, 
	  new_data, 
 	  data_variogram = input_data, 
	  block = 0, 
	  model = c("Sph", "Exp", "Gau", "Ste"), 
	  kappa = c(0.05, seq(0.2, 2, 0.1), 5, 10), 
	  fix.values = c(NA,NA,NA), 
	  remove_duplicates = TRUE, 
	  verbose = FALSE, 
	  GLS.model = NA,
      start_vals = c(NA,NA,NA),
      miscFitOptions = list(),
	  ...)

Arguments

formula formula that defines the dependent variable as a linear model of independent variables; suppose the dependent variable has name ‘z’, for ordinary and simple kriging use the formula ‘z~1’; for simple kriging also define ‘beta’ (see below); for universal kriging, suppose ‘z’ is linearly dependent on ‘x’ and ‘y’, use the formula ‘z~x+y’.
input_data An object of the SpatialPointsDataFrame-class containing the data to be interpolated.
new_data A sp object containing the prediction locations. new_data can be a points set, a grid or a polygon. Must not contain NA’s. If this object is not provided a default is calculated. This is done by taking the convex hull ofinput_data and placing around 5000 gridcells in that convex hull.
data_variogram An optional way to provide a different dataset for the building of the variogram then for the spatial interpolation.
block Use this parameter to pass on a specification for the block size. e.g. c(1000,1000)
model List of models that will be tested during automatic variogram fitting.
kappa List of values for the smoothing parameter of the Matern model that will be tested during automatic variogram fitting.
fix.values Can be used to fix a variogram parameter to a certain value. It consists of a list with a length of three. The items describe the fixed value for the nugget, range and sill respectively. Setting the value to NA means that the value is not fixed. Is passed on to autofitVariogram.
remove_duplicates logical, remove duplicate points from the input_data. This can take some time on large datasets.
verbose logical, if TRUE autoKrige will give extra information on the fitting process
GLS.model If a variogram model is passed on through this parameter a Generalized Least Squares sample variogram is calculated.
start_vals Can be used to give the starting values for the variogram fitting. The items describe the fixed value for the nugget, range and sill respectively. They need to be given in that order. Setting the value to NA means that the value will be automatically chosen.
miscFitOptions Additional options to set the behavior of autofitVariogram. For details see the documentation of autofitVariogram.
... arguments that are passed on to the gstat function krige.

Details

autoKrige calls the function autofitVariogram that fits a variogram model to the given dataset. This variogram model and the data are used to make predictions on the locations in new_data. The only compulsory argument is input_data. So the most simple call would of the form:

autoKrige(meuse)

autoKrige now assumes that you want to perform ordinary kriging on the first column of input_data.

autoKrige performs some checks on the coordinate systems of input_data and new_data. If one of both is NA, it is assigned the projection of the other. If they have different projections, an error is raised. If one of both has a non-projected system (i.e. latitude-longitude), an error is raised. This error is raised because ‘gstat does use spherical distances when data are in geographical coordinates, however the usual variogram models are typically not non-negative definite on the sphere, and no appropriate models are available’ (Edzer Pebesma on r-sig-geo).

When the user specifies the power model (Pow) as the model, the initial range is set to one. Note that when using the power model, the initial range is the initial power.

Value

This function returns an autoKrige object containing the results of the interpolation (prediction, variance and standard deviation), the sample variogram, the variogram model that was fitted by autofitVariogram and the sums of squares between the sample variogram and the fitted variogram model. The attribute names are krige_output, exp_var, var_model and sserr respectively.

Author(s)

Paul Hiemstra, paul@numbertheory.nl

See Also

autofitVariogram, krige

Examples

# Data preparation
data(meuse)
coordinates(meuse) =~ x+y
data(meuse.grid)
gridded(meuse.grid) =~ x+y

# Ordinary kriging, no new_data object
kriging_result = autoKrige(zinc~1, meuse)
plot(kriging_result)

# Ordinary kriging
kriging_result = autoKrige(zinc~1, meuse, meuse.grid)
plot(kriging_result)

# Fixing the nugget to 0.2
kriging_result = autoKrige(zinc~1, meuse, 
	meuse.grid, fix.values = c(0.2,NA,NA))
plot(kriging_result)

# Universal kriging
kriging_result = autoKrige(zinc~soil+ffreq+dist, meuse, meuse.grid)
plot(kriging_result)

# Block kriging
kriging_result_block = autoKrige(zinc~soil+ffreq+dist, 
	meuse, meuse.grid, block = c(400,400))
plot(kriging_result_block)

# Dealing with duplicate observations
data(meuse)
meuse.dup = rbind(meuse, meuse[1,]) # Create duplicate
coordinates(meuse.dup) = ~x+y
kr = autoKrige(zinc~dist, meuse.dup, meuse.grid)

# Extracting parts from the autoKrige object
prediction_spdf = kr$krige_output
sample_variogram = kr$exp_var
variogram_model = kr$var_model

Results

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(automap)
Loading required package: sp
Loading required package: gstat
> png(filename="/home/oogasawa/snapshot/RGM3/R_CC/result/automap/autoKrige.rd_%03d_medium.png", width=480, height=480)
> ### Name: autoKrige
> ### Title: Performs an automatic interpolation
> ### Aliases: autoKrige
> 
> ### ** Examples
> 
> # Data preparation
> data(meuse)
> coordinates(meuse) =~ x+y
> data(meuse.grid)
> gridded(meuse.grid) =~ x+y
> 
> # Ordinary kriging, no new_data object
> kriging_result = autoKrige(zinc~1, meuse)
[using ordinary kriging]
> plot(kriging_result)
> 
> # Ordinary kriging
> kriging_result = autoKrige(zinc~1, meuse, meuse.grid)
[using ordinary kriging]
> plot(kriging_result)
> 
> # Fixing the nugget to 0.2
> kriging_result = autoKrige(zinc~1, meuse, 
+ 	meuse.grid, fix.values = c(0.2,NA,NA))
[using ordinary kriging]
> plot(kriging_result)
> 
> # Universal kriging
> kriging_result = autoKrige(zinc~soil+ffreq+dist, meuse, meuse.grid)
[using universal kriging]
> plot(kriging_result)
> 
> # Block kriging
> kriging_result_block = autoKrige(zinc~soil+ffreq+dist, 
+ 	meuse, meuse.grid, block = c(400,400))
[using universal kriging]
> plot(kriging_result_block)
> 
> # Dealing with duplicate observations
> data(meuse)
> meuse.dup = rbind(meuse, meuse[1,]) # Create duplicate
> coordinates(meuse.dup) = ~x+y
> kr = autoKrige(zinc~dist, meuse.dup, meuse.grid)
Warning in autoKrige(zinc ~ dist, meuse.dup, meuse.grid) :
  Removed 1 duplicate observation(s) in input_data:
         coordinates cadmium copper lead zinc  elev       dist   om ffreq soil
1   (181072, 333611)    11.7     85  299 1022 7.909 0.00135803 13.6     1    1
139 (181072, 333611)    11.7     85  299 1022 7.909 0.00135803 13.6     1    1
    lime landuse dist.m
1      1      Ah     50
139    1      Ah     50
[using universal kriging]
> 
> # Extracting parts from the autoKrige object
> prediction_spdf = kr$krige_output
> sample_variogram = kr$exp_var
> variogram_model = kr$var_model
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>