[R] not understanding geoR "nugget" output

Melanie A. Link-Perez linkpema at muohio.edu
Tue Sep 28 22:58:56 CEST 2004

I am having difficulty understanding the output from a likfit call,
specifically the output for the nugget.  When the partial sill is non-zero,
the estimated nugget that is returned is zero.  When the partial sill is zero,
I get a non-zero nugget.  The following output may be helpful:

Estimation method: maximum likelihood

Parameters of the mean component (trend):
  beta0   beta1   beta2   beta3   beta4   beta5
 2.4299  2.5095  4.8184 -0.0084 -0.0625 -0.0057

Parameters of the spatial component:
   correlation function: spherical
      (estimated) variance parameter sigmasq (partial sill) =  1694
      (estimated) cor. fct. parameter phi (range parameter)  =  32.1
   anisotropy parameters:
      (fixed) anisotropy angle = 0  ( 0 degrees )
      (fixed) anisotropy ratio = 1

Parameter of the error component:
      (estimated) nugget =  0

Transformation parameter:
      (fixed) Box-Cox parameter = 1 (no transformation)

Maximised Likelihood:
   log.L n.params      AIC      BIC
"-98.92"      "9"  "215.8"  "224.8"

non spatial model:
   log.L n.params      AIC      BIC
"-101.5"      "8"  "219.0"  "226.9"

likfit(geodata = geodataK, trend = "2nd", ini.cov.pars = c(1700,
    50), cov.model = "sph", method.lik = "ML")

This is the code I used:

geodataK <- as.geodata(data[,c(2,3,11)], coords.col=1:2, data.col=3)
bin4 <- variog(geodataK, uvec=seq(0,163.44,l=21), max.dist=50,
estimator.type="modulus", trend="2nd"); plot(bin4, main = "(f) Potassium",
xlab = "", ylab = "")
mod1 <- likfit(cov.model="sph",geodataK, trend="2nd",ini=c(1700,50),
lines(mod1, lty=1)


I am also trying to figure out how to calculate R^2 values for the likfit
models that I fit to the semivariogram.

I am using R version 1.9.1 (rw1091) and geoR version  1.4-8 on a PC running MS
Windows XP Professional version 2002.

Many thanks,
Melanie Link-Perez
Miami University

More information about the R-help mailing list