Dear R users, I need some help in understanding the spatial correlation structure. Is there a document or paper that explains how to use spatial correlation structure such as "corExp"? Here is the problem I run into. With the spatial correlation structure: "correlation = corExp(c(10,0.8),form = ~ north + east)" I tried to define the range and nugget as 10 miles and 0.8, respectively. However, I got the error message "Error in initialize.corSpatial....Initial value for corSpatial parameters of wrong dimension". Can anyone tell me what this means? I then tried the script: "correlation = corExp(10,form = ~ north + east)" It worked. However, it seems the range "10" was not used because after I changed it to "3", I got exactly the same estimation results. I'm wondering what the right way to do this. Any advice is appreciated! Best Gary -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Need-help-understanding-the-spatial-correlation-structure-applied-in-lme-tp6049193p7580220.html Sent from the R-sig-geo mailing list archive at Nabble.com.
spatial correlation structure in lme
4 messages · Gary Dong, Edzer Pebesma
It would have helped us when you would have provided an example that was reproducible for readers of this list. I tried some things out, along that way, but didn't manage. Maybe you could try the mixed-models list: https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models If you find out how these things work, feedback to this list would be appreciated.
On 06/16/2012 04:52 AM, wudadan wrote:
Dear R users, I need some help in understanding the spatial correlation structure. Is there a document or paper that explains how to use spatial correlation structure such as "corExp"? Here is the problem I run into. With the spatial correlation structure: "correlation = corExp(c(10,0.8),form = ~ north + east)" I tried to define the range and nugget as 10 miles and 0.8, respectively.
the help pages here suggest you'd have to add nugget=TRUE to the corExp arguments.
However, I got the error message "Error in initialize.corSpatial....Initial value for corSpatial parameters of wrong dimension". Can anyone tell me what this means? I then tried the script: "correlation = corExp(10,form = ~ north + east)" It worked. However, it seems the range "10" was not used because after I changed it to "3", I got exactly the same estimation results. I'm wondering what the right way to do this. Any advice is appreciated! Best Gary -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Need-help-understanding-the-spatial-correlation-structure-applied-in-lme-tp6049193p7580220.html Sent from the R-sig-geo mailing list archive at Nabble.com.
_______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Edzer Pebesma Institute for Geoinformatics (ifgi), University of M?nster Weseler Stra?e 253, 48151 M?nster, Germany. Phone: +49 251 8333081, Fax: +49 251 8339763 http://ifgi.uni-muenster.de http://www.52north.org/geostatistics e.pebesma at wwu.de
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On 06/16/2012 07:01 PM, Gary Dong wrote:
Thanks for your advice. Let me re-phrase my question with a reproducible example. Same message was also posted to the mixed-model list. Sorry for the cross-posting. The example and data are from UCLA's R FAQ webpage. The link for the webpage is: http://www.ats.ucla.edu/stat/r/faq/spatial_regression.htm First, following the instructions on the webpage, I did the following??? install.packages("nlme") library(nlme) spdata <- read.table("http://www.ats.ucla.edu/stat/R/faq/thick.csv", header = T, sep = ",") dummy <- rep(1, 75) spdata <- cbind(spdata, dummy) ### estimated the null model ### soil.model <- lme(fixed = thick ~ soil, data = spdata, random = ~ 1 | dummy, method = "ML") summary(soil.model) plot(Variogram(soil.model,form=~north+east)) ### then updated the model by the spatial correlation structure #### soil.gaus <- update(soil.model, correlation=corGaus(1,form=~north+east)) summary(soil.gaus) plot(Variogram(soil.gaus,form=~north+east)) *My first question is*: the variogram of soil.gaus indicates a range of 40, but the estimated range is 20.43725. Does this mean the model "soil.gaus" failed?
no, it means that the range parameter is not identical to the value you interpret from the plot as range. This is usual for Gaussian and exponential models and some others, try: library(gstat) show.vgms(range=20, model="Gau", max=50)
Next, I define the range and nugget manually as below. The variogram of soil.model indicates a range at 40 and nugget at about 0.1. soil.gaus.1 <- update(soil.model, correlation=corGaus(c(40,0.1),form=~north+east,nugget=T)) summary(soil.gaus.1) plot(Variogram(soil.gaus.1,form=~north+east)) The estimated range looks right (very close to 40). But the estimated nugget and variogram plot still look weird. *So my question is*: what I can do next step to improve the model? Any advice would be greatly appreciated! Best Gary On Sat, Jun 16, 2012 at 2:23 AM, Edzer Pebesma < edzer.pebesma at uni-muenster.de> wrote:
It would have helped us when you would have provided an example that was reproducible for readers of this list. I tried some things out, along that way, but didn't manage. Maybe you could try the mixed-models list:
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models If you find out how these things work, feedback to this list would be appreciated. On 06/16/2012 04:52 AM, wudadan wrote: Dear R users, I need some help in understanding the spatial correlation structure. Is there a document or paper that explains how to use spatial correlation structure such as "corExp"? Here is the problem I run into. With the spatial correlation structure: "correlation = corExp(c(10,0.8),form = ~ north + east)" I tried to define the range and nugget as 10 miles and 0.8, respectively. the help pages here suggest you'd have to add nugget=TRUE to the corExp arguments. However, I got the error message "Error in initialize.corSpatial....Initial value for corSpatial parameters of wrong dimension". Can anyone tell me what this means? I then tried the script: "correlation = corExp(10,form = ~ north + east)" It worked. However, it seems the range "10" was not used because after I changed it to "3", I got exactly the same estimation results. I'm wondering what the right way to do this. Any advice is appreciated! Best Gary -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Need-help-understanding-the-spatial-correlation-structure-applied-in-lme-tp6049193p7580220.html Sent from the R-sig-geo mailing list archive at Nabble.com. _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo -- Edzer Pebesma Institute for Geoinformatics (ifgi), University of M??nster Weseler Stra??e 253, 48151 M??nster, Germany. Phone: +49 251 8333081, Fax: +49 251 8339763 http://ifgi.uni-muenster.de http://www.52north.org/geostatistics e.pebesma at wwu.de _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
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_______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Edzer Pebesma Institute for Geoinformatics (ifgi), University of M?nster Weseler Stra?e 253, 48151 M?nster, Germany. Phone: +49 251 8333081, Fax: +49 251 8339763 http://ifgi.uni-muenster.de http://www.52north.org/geostatistics e.pebesma at wwu.de