fmesher question- error with R. 4.3

[Nayantara Wijayanandana]

Hello,

Please could you let me know if there is a workaround to upgrading my R version (4.3.1) so my model still runs with INLA.

Everything was working fine upto this point. But I started to get an error recently when I tried to rerun a model. I think this has to do with the version of fmesher, but maybe I am wrong. At this moment in time, I do not want to upgrade everything so would be grateful for any help to hone in on the problem.  I uploaded the version of INLA that was indicated for R 4.3.

Many thanks,

Nayantara

> library(INLA)
Error: package or namespace load failed for ‘INLA’:
 object ‘fm_identical_CRS’ is not exported by 'namespace:fmesher'
In addition: Warning message:
package ‘INLA’ was built under R version 4.3.3 

#Stack creation and inla analysis
s.index <- inla.spde.make.index(name="spatial.field", n.spde=spde$n.spde)
A.est = inla.spde.make.A(mesh=mesh,
                         loc=as.matrix(df.st[,c("x","y")]))
stack.est = inla.stack(data=list(obs=df.st$obs),
                       A=list(A.est,
                              1),
                       effects=list(c(s.index, list(Intercept=1)),
                                    list(df.st[,-1])),
                       tag='stdata')

[INLA help]

Upgrade to R-4.5 …

—

Haavard Rue

Helpdesk

he...@r-inla.org

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[Nayantara Wijayanandana]

Hello,

Thank you for the quick response. Yes, in parallel I upgraded to  R 4.5.1. on my desktop so I can compare.  I got this error :

Error in UseMethod("fm_dof") : 

  no applicable method for 'fm_dof' applied to an object of class "inla.mesh"

 

> packageVersion("INLA")

[1] ‘25.6.7’

> packageVersion("fmesher")

[1] ‘0.5.0.9004’

[Havard Rue]

When you upgrade to R 4.5, you need to reinstall all packages. Better, remove all, and then reinstall

—

Håvard Rue
Professor of Statistics
Chair of Statistics Program, CEMSE Division
King Abdullah University of Science and Technology
Thuwal 23955-6900, Saudi Arabia

Email: haava...@kaust.edu.sa
Office: +966 (0)12 808 0640
Mobile: +966 (0)54 470 0421
Research group: bayescomp.kaust.edu.sa
R-INLA project: www.r-inla.org
Zoom: kaust.zoom.us/my/haavard.rue

To view this discussion, visit https://groups.google.com/d/msgid/r-inla-discussion-group/8BEF8ACD-DE26-43A0-9613-97E6A5922D21%40gmail.com.

[Finn Lindgren]

You likely have a very very old, stored mesh object?

Best solution is to regenerate the mesh to get a modern object with the correct S3 class.

Fmesher also has conversion tools that may work, like

fm_as_fm(mesh)

the old inla.mesh class does have a conversion;method, according to

https://inlabru-org.github.io/fmesher/reference/fm_as_fm.html

Finn