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List:       r-help
Subject:    [R] Gam with mrf smoother (mgcv)
From:       Giulia Carella <Giulia.Carella () lsce ! ipsl ! fr>
Date:       2018-02-26 14:06:28
Message-ID: 44e87bc6-9d0a-860f-7055-9d1cf39e01f8 () lsce ! ipsl ! fr
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Hallo,

I want to use gam from the mgcv package with a mrf smoother.

This is my data set (`x`)

              y                   id
        1   0.6684496   1
        2   0.6684496   2
        3   0.6684496   3
        4   0.6684496   4
        5   0.6684496   5
        6   0.6684496   6
        7   0.6684496   7
        8   0.5879492   8
        9   0.5879492   9
        10 0.5879492 10
        11 0.5879492 11
        12 0.5879492 12
        13 0.5879492 13
        14 0.5879492 14
        15 0.6445448 15
        16 0.6445448 16
        17 0.6445448 17
        18 0.6445448 18
        19 0.6445448 19
        20 0.6445448 20
        21 0.6445448 21
        22 0.5815767 22
        23 0.5815767 23
        24 0.5815767 24
        25 0.5815767 25
        26 0.5815767 26
        27 0.5815767 27
        28 0.5815767 28
        29 0.6636673 29
        30 0.6636673 30
        31 0.6636673 31
        32 0.6636673 32
        33 0.6636673 33
        34 0.6636673 34
        35 0.6636673 35
        36 0.4249320 36
        37 0.4249320 37
        38 0.4249320 38
        39 0.4249320 39
        40 0.4249320 40
        41 0.4249320 41
        42 0.4249320 42

and this is my neighbouring structure (nb)

        $`1`
        [1] 1 2 3 4 5 6 7

        $`2`
        [1] 1 2 3 4 5 6 7

        $`3`
        [1] 1 2 3 4 5 6 7

        $`4`
        [1] 1 2 3 4 5 6 7

        $`5`
        [1] 1 2 3 4 5 6 7

        $`6`
        [1] 1 2 3 4 5 6 7

        $`7`
        [1] 1 2 3 4 5 6 7

        $`8`
        [1]   8   9 10 11 12 13 14

        $`9`
        [1]   8   9 10 11 12 13 14

        $`10`
        [1]   8   9 10 11 12 13 14

        $`11`
        [1]   8   9 10 11 12 13 14

        $`12`
        [1]   8   9 10 11 12 13 14

        $`13`
        [1]   8   9 10 11 12 13 14

        $`14`
        [1]   8   9 10 11 12 13 14

        $`15`
        [1] 15 16 17 18 19 20 21

        $`16`
        [1] 15 16 17 18 19 20 21

        $`17`
        [1] 15 16 17 18 19 20 21

        $`18`
        [1] 15 16 17 18 19 20 21

        $`19`
        [1] 15 16 17 18 19 20 21

        $`20`
        [1] 15 16 17 18 19 20 21

        $`21`
        [1] 15 16 17 18 19 20 21

        $`22`
        [1] 22 23 24 25 26 27 28

        $`23`
        [1] 22 23 24 25 26 27 28

        $`24`
        [1] 22 23 24 25 26 27 28

        $`25`
        [1] 22 23 24 25 26 27 28

        $`26`
        [1] 22 23 24 25 26 27 28

        $`27`
        [1] 22 23 24 25 26 27 28

        $`28`
        [1] 22 23 24 25 26 27 28

        $`29`
        [1] 29 30 31 32 33 34 35

        $`30`
        [1] 29 30 31 32 33 34 35

        $`31`
        [1] 29 30 31 32 33 34 35

        $`32`
        [1] 29 30 31 32 33 34 35

        $`33`
        [1] 29 30 31 32 33 34 35

        $`34`
        [1] 29 30 31 32 33 34 35

        $`35`
        [1] 29 30 31 32 33 34 35

        $`36`
        [1] 36 37 38 39 40 41 42

        $`37`
        [1] 36 37 38 39 40 41 42

        $`38`
        [1] 36 37 38 39 40 41 42

        $`39`
        [1] 36 37 38 39 40 41 42

        $`40`
        [1] 36 37 38 39 40 41 42

        $`41`
        [1] 36 37 38 39 40 41 42

        $`42`
        [1] 36 37 38 39 40 41 42

However, when I run

        b <- gam(y ~ s(id,bs="mrf",xt=list(nb=nb)),data=x,method="REML")

I get the following error:

Error in initial.sp(w * x, S, off) : S[[1]] matrix is not +ve definite.

Why is the penalty matrix non semi-positive definite? Am I defining 
something wrong?

Many thanks in advance

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