[R-sig-Geo] Warning in fit.variogram: value out of range in 'bessel k' | automap and gstat packages

Mon Sep 16 11:11:15 CEST 2019

Hi Frederico,

gstat does not have different behaviour, because autofitVariogram is using fit.variogram, after some preprocessing. You get the convergency problems with fit.variogram because you don't supply start values for the variogram, which is done in the preprocessing of autofitVariogram.

Cheers,

Jon

--
Jon Olav Sk�ien
European Commission
Joint Research Centre � JRC.E.1
Disaster Risk Management Unit
Building 26b 1/144 | Via E.Fermi 2749, I-21027 Ispra (VA) Italy, TP 267
jon.skoien using ec.europa.eu<https://remi.webmail.ec.europa.eu/owa/redir.aspx?C=O12RUARdbvGA3WF3zGoSV0j5xMoZlQcIEwiS4Y9G8jzXRqCCC1HUCA..&URL=mailto%3ajon.skoien%40jrc.ec.europa.eu> Tel:  +39 0332 789205 Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission.

________________________________
From: Frederico Faleiro <fvfaleiro using gmail.com>
Sent: 13 September 2019 23:16:22
To: SKOIEN Jon (JRC-ISPRA)
Cc: RsigGeo
Subject: Re: [R-sig-Geo] Warning in fit.variogram: value out of range in 'bessel k' | automap and gstat packages

Hi Jon and others,

thank you for your help. The problem is really in the Ste model (Matern, M. Stein's parameterization). The warning only happens
when I execute this model. However in the gstat with the same parameters for lambda have problem of convergency. Do you think the gstat have different bevavior to the same issue?

av <- autofitVariogram(jan~1, pr, model = "Ste", verbose = T)
# In fit.variogram(experimental_variogram, model = vgm(psill = psill,  ... :  value out of range in 'bessel_k'

# define the same kappa values of automap
seq.k <- c(0.05, seq(0.2, 2, 0.1), 5, 10)
ve <- variogram(jan~1, pr)
v <- fit.variogram(v, vgm("Ste"), fit.kappa = seq.k)
Warning messages:
1: In fit.variogram(object, model, fit.sills = fit.sills, fit.ranges = fit.ranges,  :
  No convergence after 200 iterations: try different initial values?
2: In fit.variogram(object, model, fit.sills = fit.sills, fit.ranges = fit.ranges,  :
  No convergence after 200 iterations: try different initial values?
3: In fit.variogram(o, m, fit.kappa = FALSE, fit.method = fit.method,  :
  No convergence after 200 iterations: try different initial values?

Best regards,

Frederico

On Wed, Sep 11, 2019 at 7:02 AM <Jon.SKOIEN using ec.europa.eu<mailto:Jon.SKOIEN using ec.europa.eu>> wrote:

Frederico,

I don't think you need to worry about this warning in this case. autofitVariogram tests a lot of variogram models (and different kappa-values) in the search for the best one, and then fit.variogram tries to optimize the parameters based on these. It seems the warnings were generated in the C-code of gstat, based on some of the tested kappa-values for the Matern variogram (Stein implementation). It also seems that these kappa values did not give good fits to the sample variogram, so you did not get the warning from the best fit variogram in this case.

Hope this helps,

Jon

--
Jon Olav Sk�ien
European Commission
Joint Research Centre � JRC.E.1
Disaster Risk Management Unit
Building 26b 1/144 | Via E.Fermi 2749, I-21027 Ispra (VA) Italy, TP 267
jon.skoien using ec.europa.eu<https://remi.webmail.ec.europa.eu/owa/redir.aspx?C=O12RUARdbvGA3WF3zGoSV0j5xMoZlQcIEwiS4Y9G8jzXRqCCC1HUCA..&URL=mailto%3ajon.skoien%40jrc.ec.europa.eu> Tel:  +39 0332 789205 Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission.

________________________________
From: R-sig-Geo <r-sig-geo-bounces using r-project.org<mailto:r-sig-geo-bounces using r-project.org>> on behalf of Frederico Faleiro <fvfaleiro using gmail.com<mailto:fvfaleiro using gmail.com>>
Sent: 09 September 2019 21:28:32
To: RsigGeo
Subject: [R-sig-Geo] Warning in fit.variogram: value out of range in 'bessel k' | automap and gstat packages

Dear list,

I am trying make an interpolation with the function autoKrige from the
package automap, but I received more than 50 times the following warning
message:

In fit.variogram(experimental variogram, model = vgm(psill = psill, ... :
value out of range in 'bessel k'

I have tryed identify it in the code of fit.variogram and vgm from the
gstat package, but they do not have any warning about it in the code. Then
I imagine the warning is from another function.
I fitted the variogram automatically in the automap and after I fitted in
the gstat to check if there is the same warning for that parameters, but in
the last I do not have any warning. When I check the variogram model, it
has a good fit apparently. I provided the reproductible example below.

Do you know the consequences of this warning and how can I avoid it? I
would like to use the automap package because I need interpolate many other
files like this.

# example
library(automap)
library(sp)

# download the data in:
https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1L33-5FQgpNMdwvWff-5FuMrwhl-5FKCajrtlVe_view-3Fusp-3Dsharing&d=DwICAg&c=8NwulVB6ucrjuSGiwL_ckQ&r=DA6jV5X00Z1YpyMh4OS79xeSQGErBqY83CBz841DNnU&m=YlpT3yKlbNVLvXMp08O8X1LkniHGXTzJeLDHLTotwOI&s=U2z98vHb1mpKhKJ9UXA0RUrPi6r6IXibq1cuuyB0jWY&e=
# read the data
pr <- read.table('pr_monC.txt', header = TRUE, sep = "\t")
coordinates(pr) <- ~long+lat
# read the grid
gr <- read.table('grid.txt' , header = TRUE, sep = '\t')
gridded(gr) <-  ~long+lat

# automatic fit variogram with automap
av <- autofitVariogram(jan~1, pr)
# warnings message:   In fit.variogram(experimental variogram, model =
vgm(psill = psill, ... : value out of range in 'bessel k'
plot(av) # get in the graph the parameters to fit the variogram

# fit variogram in gstat with the model parameters from autofitVariogram to
check if there is any warning message too
ve <- variogram(jan~1, pr)
v <- fit.variogram(ve, vgm(psill = 9723, model = "Ste", range = 20, nugget
= 194, kappa = 0.8))
# it does not produce any warning
plot(ve, v)

Best regards,

Frederico

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