krige() function with SpatialPointsDataFrame in R

[Jouline]

I would like to make some kriging in a belgian territory.

I got a data set called clean.donnees.Ni after removing outliers and NAvalues.

I first tried simply with this, but got this warning as result :

Ni.krig <- krige(formula = Ni~1,
                 data = clean.donnees.Ni,
                 locations = ~x+y,
                 newdata = krig.grid, 
                 model = Ni.vg.fit)

Warnings : Covariance matrix singular at location [50686, 156893,0]: skipping

I found on other topics that I probably got points at the same location.
(interpolation - R gstat krige() - Covariance matrix singular at location [5.88,47.4,0]: skipping - Geographic Information Systems Stack Exchange)

They advice to use this to remove points on the same location:

clean.donnees.Ni <- clean.donnees.Ni[-zerodist(clean.donnees.Ni)[,1],]

When I did this, I finally thought I could make krige() work, but instead it nows returns me this error :

Ni.krig <- krige(formula = Ni~1,
                 data = clean.donnees.Ni,
                 locations = ~x+y,
                 newdata = krig.grid, 
                 model = Ni.vg.fit)

Error in `coordinates<-`(`*tmp*`, value = locations) : 
  setting coordinates cannot be done on Spatial objects, where they have already been set

Because I had to transform clean.donnees.Ni in a SpatialPointsDataFrame, locations can't read ~x+y anymore.

Does anyone knows how to makes kriging work ?

[nirgrahamuk]

@Jouline

krige(formula = Ni~1,
                 data = clean.donnees.Ni,
                 locations = ~x+y,
                 newdata = krig.grid, 
                 model = Ni.vg.fit)

try

krige(formula = Ni~1,
                 locations = clean.donnees.Ni,
                 newdata = krig.grid, 
                 model = Ni.vg.fit)

[nirgrahamuk]

Hi!

To help us help you, could you please prepare a reproducible example (reprex) illustrating your issue? Please have a look at this guide, to see how to create one:

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

[Jouline]

> d = data.frame(x=runif(100), y=runif(100), Z=rnorm(100))
> coordinates(d)=~x+y
> 
> k = krige(formula = Z~1, data=d, locations=~x+y, newdata=d)
Error in `coordinates<-`(`*tmp*`, value = locations) : 
  setting coordinates cannot be done on Spatial objects, where they have already been set
> 
> k = krige(formula = Z~1, locations=d, newdata=d)
[inverse distance weighted interpolation]

That's a simpler example, and actually your solution should work.
With my error

Ni.krig <- krige(formula = Ni~1,
                   locations = clean.donnees.Ni,
                   newdata = krig.grid, 
                   model = Ni.vg.fit)

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'obj' in selecting a method for function 'coordinates': trying to get slot "bbox" from an object (class "data.table") that is not an S4 object 

there is something strange, as you can see my clean.donnees.Ni is well a S4 object :

> typeof(clean.donnees.Ni) 
[1] "S4"

[nirgrahamuk]

the type is less important than the class. but I'm afraid we will get into a strange dance without a clear example of your issue to investigate

[Jouline]

I finally found my mistake, and your answer is the right to my question !
(I had to transform krig.grid to S4 object too)