spatstat/spatstat.linnet

Problem with the inclusion of lintess objects in lppm

Closed this issue · 5 comments

agila5 commented

Dear all, I think I've found a possible problem with the inclusion of lintess objects in a model estimated by lppm. For example:

library(spatstat)
#> Loading required package: spatstat.data
#> Loading required package: spatstat.geom
#> spatstat.geom 3.2-2
#> Loading required package: spatstat.random
#> spatstat.random 3.1-5
#> Loading required package: spatstat.explore
#> Loading required package: nlme
#> spatstat.explore 3.2-1
#> Loading required package: spatstat.model
#> Loading required package: rpart
#> spatstat.model 3.2-4
#> Loading required package: spatstat.linnet
#> spatstat.linnet 3.1-1
#> 
#> spatstat 3.0-6 
#> For an introduction to spatstat, type 'beginner'

toy_points <- rpoislpp(20, simplenet)
toy_tess <- lintess(
  L = simplenet, 
  df = data.frame(
    seg = 1:10, 
    t0 = 0, 
    t1 = 1, 
    tile = c("A", "B")
  )
)

lppm(toy_points ~ toy_tess)
#> Error in mpl.get.covariates(covariates, P, Pname, covfunargs): Each entry in the list 'covariates' should be an image, a function, a window, a tessellation or a single number

A possible workaround I've found:

toy_linfun <- as.linfun(toy_tess)
lppm(toy_points ~ toy_linfun)
#> Point process model on linear network
#>  Fitted to point pattern dataset 'toy_points'
#> 
#> Nonstationary Poisson process
#> 
#> Log intensity:  ~toy_linfun
#> 
#> Fitted trend coefficients:
#> (Intercept) toy_linfunB 
#>    3.311431    0.123307 
#> 
#>             Estimate      S.E.    CI95.lo  CI95.hi Ztest       Zval
#> (Intercept) 3.311431 0.1601282  2.9975856 3.625276   *** 20.6798800
#> toy_linfunB 0.123307 0.2176698 -0.3033181 0.549932        0.5664863
#> 
#> Domain: Linear network with 10 vertices and 10 lines
#> Enclosing window: rectangle = [0, 1] x [0, 1] units

Created on 2023-07-12 with reprex v2.0.2

Am I doing something wrong in the first call to lppm? Is the workaround ok? In any case, thank you very much for maintaining this amazing set of packages.

rubak commented

Hi Andrea,
Sorry for the radio silence. This is just to confirm that I can reproduce the problem and we will fix it for the next release. Thanks for reporting!
Best,
Ege

baddstats commented

Currently lppm does not support covariates which are objects of class lintess. The documentation does not say that these are supported (although admittedly the help for lppm does mention "tessellations", it means that objects of class tess are supported). I agree that it would be nice if lppm handled lintess covariates.

The problem is related to the split-up of spatstat into multiple sub-packages. Models are fitted using the internal code of ppm.

I am not as confident as Ege that this can be fixed soon. I do not promise to fix it by the next release. However I will try.

rubak commented
baddstats commented

I have found a "hack" solution. Please install spatstat.model development version 3.2-4.001 or later. Then it should work.

agila5 commented

Works perfectly, thank you very much for the speedy fix!