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JenniNiku / gllvm

Generalized Linear Latent Variable Models
https://jenniniku.github.io/gllvm/
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Number of provided distance matrices should equal the number of spatially structured row effects. #174

Closed AlainZuur closed 3 months ago

AlainZuur commented 3 months ago

Bert..you must have changed something here between the CRAN version (which works fine with the code below) and the development version which throws this error: Number of provided distance matrices should equal the number of spatially structured row effects.

Any suggestions? It is the last question of the day!

Alain

' Grab the spatial coordinates. These are in km?

CoordData <- data.frame(Xkm = Fish3$X, Ykm = Fish3$Y) CoordData <- as.matrix(CoordData) CoordData

' Define a group structure

GroupStruc <- data.frame(Group = 1:nrow(Fish3))

' Then this should do the job.

M10 <- gllvm(y = SpecData, X = CovX.s, num.lv = 0, num.RR = 2, lv.formula = ~ Altitude + LogSlope + MMDischarge + pH + Calcium + Nitrate + Ammonium + DisOxygen + OxygenDemand, family = "poisson", studyDesign = GroupStruc, row.eff = ~corExp(1 | Group), dist = CoordData,

corWithin = FALSE,

         control = list(optimizer = "alabama"), #alabama
         control.start = list(n.init = 5, jitter.var = 0.1))
BertvanderVeen commented 3 months ago

See ?gllvm documentation, and "news" for what's changed. "dist" should be a list. Try that, see if it solves your issue. This is because -technically- you can now include multiple row effects, so you could provide multiple matrices of coordinates.

I'll see later if i can do something about backwards compatibility, i.e., if you pass a single matrix to "dist" it should probably accept that too.

AlainZuur commented 3 months ago

dist = list(CoordData),

solves it. Thanks. That's it for today!