INTEGER() error

Anirban Basu

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Aug 4, 2021, 8:02:36 PM8/4/21

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Hi all,

I am trying to run a simple model:

formula <- airqlty ~ 1 + f(ID, model="bym", graph = W, hyper =

list(prec.unstruct = list(prior="loggamma", param=c(1,0.01)),

prec.spatial = list(prior="loggamma", param=c(1,0.001 ))))

mod<-inla(formula, family="gaussian", data=leafdata)

But it gives me an error:

Error in card(neighbours) :

INTEGER() can only be applied to a 'integer', not a 'character'

My graph file is fine, with 3105 neighbors and corresponding weights. The neighbors are identified with corrresponding integer values. Also, ID in my dataset is an integer. I just dont know where INTEGER() is being applied. Any help is appreciated.

Thanks,

Anirban

Helpdesk

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Aug 5, 2021, 2:15:28 AM8/5/21

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I think you have a graph that is of wrong type, ie your 'W' is not a
'inla.graph' class or a numerical matrix

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Anirban Basu

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Aug 5, 2021, 12:51:00 PM8/5/21

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I created W in this way. If you have any reco as to how to differently create W, I would appreciate it.

Thanks,

us.poly<-readOGR("cb_2016_us_county_500k.shp")

# Remove counties with no neighbours

list.queen<-poly2nb(us.poly, queen=TRUE)

cards<-card(list.queen)

tr<- which(cards==0)

sub.poly<- us.poly[-tr, ]

# Merge spatial df with downloaded data.

leafmap2 <- merge(sub.poly, county_dat, by=c("GEOID"), all=FALSE)

list.queen2<-poly2nb(leafmap2, queen=TRUE)

# create inla graph

set.ZeroPolicyOption(TRUE)

W<-nb2listw(list.queen2, style="W", zero.policy=TRUE)

W

W has three elements, Style (==W), neighbours, and weights

> card(W$neighbours)

[1] 6 6 7 5 7 7 4 6 6 4 9 7 5 4 6 7 6 7 5 6 6 7 5 6 5 7

[27] 6 9 6 7 6 7 6 5 6 6 9 7 5 6 7 6 5 5 5 8 4 6 4 6 5 3

[53] 5 6 6 6 7 7 5 6 5 6 4 5 5 8 4 6 4 4 9 7 2 10 7 5 4 4

[79] 6 6 6 5 3 9 4 8 7 4 5 7 5 7 8 6 6 5 9 6 4 8 7 5 8 9

[105] 3 6 6 6 4 5 6 6 9 7 6 7 5 6 6 6 7 5 6 5 7 4 4 5 7 7

[131] 6 4 7 6 7 4 6 6 6 7 6 5 7 6 7 6 6 8 6 8 7 6 5 8 6 6

[157] 6 5 8 6 6 7 6 5 8 6 7 6 5 5 4 4 6 5 4 5 6 4 6 8 1 3

[183] 4 9 3 3 4 6 6 8 1 6 3 2 6 6 9 6 5 6 8 7 6 8 7 6 5 6

[209] 7 8 6 5 8 6 7 7 5 6 9 3 4 6 6 5 5 6 4 5 5 6 7 6 3 6

[235] 5 4 6 8 8 3 6 6 2 5 6 7 1 5 5 7 6 6 5 4 3 6 5 3 8 7

[261] 8 5 5 3 5 5 7 5 8 6 3 6 6 8 8 5 4 4 4 5 5 7 6 6 8 6

[287] 4 5 8 5 8 7 7 5 5 5 7 1 6 5 7 6 4 4 7 7 5 6 6 7 7 5

[313] 5 7 6 7 6 10 5 5 6 5 5 7 6 7 4 7 5 5 6 7 3 5 3 5 5 7

[339] 6 4 7 6 6 7 6 6 8 7 6 6 6 7 6 7 5 7 7 7 6 6 6 5 6 11

[365] 6 6 5 4 7 2 8 6 6 8 5 2 7 4 5 4 8 5 5 5 7 4 4 6 8 7

[391] 6 7 6 6 6 6 4 1 7 7 6 4 6 7 6 6 6 6 6 6 4 8 6 2 4 9

[417] 4 4 8 8 3 6 6 5 7 3 6 6 6 3 6 6 6 6 6 7 6 6 7 6 6 7

[443] 4 5 7 5 5 6 7 6 7 4 7 3 6 6 4 4 4 5 6 5 7 7 3 3 5 4

[469] 3 7 4 2 8 6 5 6 6 7 9 5 5 5 6 5 5 7 5 5 4 4 3 3 6 3

[495] 6 7 7 7 4 6 7 8 5 5 7 7 6 10 4 4 6 7 7 6 7 5 7 7 6 6

[521] 5 4 6 13 7 9 6 7 4 6 4 3 5 4 3 6 5 6 6 4 9 5 8 5 8 6

[547] 6 6 7 4 6 5 6 5 6 6 6 6 5 7 6 6 6 6 7 6 5 5 6 5 6 7

[573] 7 5 6 6 7 5 7 6 6 6 7 7 7 6 6 6 6 6 5 6 6 5 4 7 5 4

[599] 7 6 3 6 5 6 7 7 6 1 3 4 6 7 6 5 7 6 4 6 8 9 7 5 7 5

[625] 6 6 6 7 6 8 6 7 5 8 6 6 6 7 6 7 6 7 6 5 7 4 8 8 3 5

[651] 7 4 5 5 6 7 6 4 7 5 6 6 6 7 5 6 8 7 6 4 3 7 6 9 6 6

[677] 7 7 6 8 7 6 6 7 4 4 4 6 4 6 7 7 6 4 5 4 7 8 5 6 5 6

[703] 4 6 5 3 7 6 4 2 5 5 4 6 6 5 6 7 7 7 2 7 7 5 7 6 4 6

[729] 7 8 7 4 5 4 5 5 6 6 5 6 8 5 8 5 8 6 4 6 7 7 6 6 6 6

[755] 6 7 8 6 8 5 4 5 7 9 6 6 9 7 6 7 5 5 6 6 5 8 7 7 7 4

[781] 6 8 9 6 5 9 5 6 6 7 6 6 7 8 6 7 6 5 6 7 5 6 5 4 6 7

[807] 8 6 6 7 6 5 6 8 8 7 5 4 7 5 5 5 6 5 9 8 6 6 6 8 5 6

[833] 7 5 7 7 5 5 6 5 6 5 5 6 7 8 6 7 5 5 4 5 5 5 7 6 4 6

[859] 6 6 5 8 5 7 4 5 5 8 5 4 6 6 4 4 4 4 8 3 4 5 3 7 7 4

[885] 9 7 6 7 8 2 2 3 6 2 10 6 5 8 7 7 8 5 5 7 5 4 7 7 6 7

[911] 9 2 7 8 8 6 4 5 6 5 6 7 6 7 7 6 4 4 5 5 4 7 5 6 5 6

[937] 7 4 8 8 8 6 6 6 5 6 6 5 5 4 6 6 5 6 8 7 6 7 3 7 8 8

[963] 8 7 6 4 9 7 7 5 4 5 2 8 6 5 5 2 6 8 7 6 4 7 7 6 7 7

[989] 3 5 7 7 6 5 7 7 7 5 7 5

[ reached getOption("max.print") -- omitted 2104 entries ]

Helpdesk

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Aug 5, 2021, 12:59:27 PM8/5/21

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I don't think 'nb2listw' gives a valid representation.

nb2INLA ?

Virgilio Gómez-Rubio

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Aug 5, 2021, 1:26:34 PM8/5/21

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Hi,

‘nb2mat’ will take an ‘nb’ object and create an adjacency matrix that INLA can take. ‘listw2mat’ will create a weight matrix from a list object. Also, you can convert these matrices into sparse matrices with as(matrix, “Matrix”), for example.

Best,

Virgilio

Anirban Basu

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Aug 5, 2021, 2:03:20 PM8/5/21

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Thanks a lot. It seems to work if I do:

W<-nb2listw(list.queen2, style="W", zero.policy=TRUE)

WW<-listw2mat(W)

and use WW instead of W.

But it creates a new problem when running inla which says :

" Error in inla(formula, family = "gaussian", data = leafdata) : f(GEOID). Covariate does not match 'values' 3037 times.", which is strange because my WW is of 3015x3015 dimension, and my data leafdata also have 3015 rows.

Anirban

Anirban Basu

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Aug 5, 2021, 2:31:58 PM8/5/21

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Ok, I have fixed that problem by creating a new ID that just runs from 1 to NROW(data).

A

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