Fwd: spatial analysis with dbMEM

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Fwd: spatial analysis with dbMEM

Andrew Halford
Hi Listers,

I am trying to wrap my head around spatial eigenvector analyses and have
been trying to recreate the example code attached to the dbmem{adespatial}
documentation.

I am getting an error message when I try to run the following... The data
is drawn from the oribatid dataset.

data(oribatid)

mite <- oribatid$fau
mite.xy <- oribatid$xy
mite.dbmem1 <- dbmem(mite.xy, thresh=1.012, MEM.autocor = "non-null",
silent = FALSE)
s.label(mite.xy, nb = attr(mite.dbmem1, "listw"))

Error in s.label(mite.xy, nb = attr(mite.dbmem1, "listw")) :
  unused argument (nb = attr(mite.dbmem1, "listw"))
I dont know what the nb argument is here?

# Plot maps of the first 3 dbMEM eigenfunctions
s.value(mite.xy, mite.dbmem1[,1:3])

Error in s.value(mite.xy, mite.dbmem1[, 1:3]) :
  Non equal row numbers 70 3


I checked the mite.xy and mite.dbmem1 data and they both have 70 rows?

Andy



--
Andrew Halford Ph.D
Research Scientist (Kimberley Marine Parks)
Dept. Parks and Wildlife
Western Australia

Ph: +61 8 9219 9795 <+61%208%209219%209795>
Mobile: +61 (0) 468 419 473 <+61%20468%20419%20473>



--
Andrew Halford Ph.D
Research Scientist (Kimberley Marine Parks)
Dept. Parks and Wildlife
Western Australia

Ph: +61 8 9219 9795
Mobile: +61 (0) 468 419 473

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Re: Fwd: spatial analysis with dbMEM

Aaron Hogan
Hi Andy,

I am probably not the most qualified person to answer this, but I think I
may have a solution to your issue.


1.  It seems that nb is an old (or alternative) way to specify the labels
for the plot.  The documentation suggests using label.  I could not find nb
defined and was rarely used in:
https://cran.r-project.org/web/packages/adegraphics/adegraphics.pdf
<https://cran.r-project.org/web/packages/adegraphics/adegraphics.pdf>

2.  This example helped me better understand the syntax of the s.label
function:

data(mafragh, package = "ade4")
g2 <- s.label(mafragh$xy, nb = mafragh$nb, paxes.draw = FALSE)

You can see that both the $nb list and $xy dataframe have the same number
of observations (which is important- as you point out).

3.  you can extract the list from the mite data using:   attr(mite.dbmem1,
"listw")$neighbours

so putting it all together:

s.label(mite.xy, label = attr(mite.dbmem1, "listw")$neighbours)


alternatively (making the list an object named mite.nb):

mite.nb <- attr(mite.dbmem1, "listw")$neighbours
s.label(mite.xy, label = mite.nb)



Code generated the plot for me.
I hope this helps,
Best,

Aaron Hogan
(970) 485-1412
[hidden email]

On Mon, Jan 16, 2017 at 9:50 PM, Andrew Halford <[hidden email]>
wrote:

> Hi Listers,
>
> I am trying to wrap my head around spatial eigenvector analyses and have
> been trying to recreate the example code attached to the dbmem{adespatial}
> documentation.
>
> I am getting an error message when I try to run the following... The data
> is drawn from the oribatid dataset.
>
> data(oribatid)
>
> mite <- oribatid$fau
> mite.xy <- oribatid$xy
> mite.dbmem1 <- dbmem(mite.xy, thresh=1.012, MEM.autocor = "non-null",
> silent = FALSE)
> s.label(mite.xy, nb = attr(mite.dbmem1, "listw"))
>
> Error in s.label(mite.xy, nb = attr(mite.dbmem1, "listw")) :
>   unused argument (nb = attr(mite.dbmem1, "listw"))
> I dont know what the nb argument is here?
>
> # Plot maps of the first 3 dbMEM eigenfunctions
> s.value(mite.xy, mite.dbmem1[,1:3])
>
> Error in s.value(mite.xy, mite.dbmem1[, 1:3]) :
>   Non equal row numbers 70 3
>
>
> I checked the mite.xy and mite.dbmem1 data and they both have 70 rows?
>
> Andy
>
>
>
> --
> Andrew Halford Ph.D
> Research Scientist (Kimberley Marine Parks)
> Dept. Parks and Wildlife
> Western Australia
>
> Ph: +61 8 9219 9795 <+61%208%209219%209795>
> Mobile: +61 (0) 468 419 473 <+61%20468%20419%20473>
>
>
>
> --
> Andrew Halford Ph.D
> Research Scientist (Kimberley Marine Parks)
> Dept. Parks and Wildlife
> Western Australia
>
> Ph: +61 8 9219 9795
> Mobile: +61 (0) 468 419 473
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>

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Re: Fwd: spatial analysis with dbMEM

THIOULOUSE JEAN
In reply to this post by Andrew Halford
Hi

You need to load the adegraphics package AFTER loading the ade4 and adespatial packages.

There are two versions of the s.label function : one in the ade4 package and one in the adegraphics package. The one you need here is the second one.

Jean


> Le 17 janv. 2017 à 03:50, Andrew Halford <[hidden email]> a écrit :
>
> Hi Listers,
>
> I am trying to wrap my head around spatial eigenvector analyses and have
> been trying to recreate the example code attached to the dbmem{adespatial}
> documentation.
>
> I am getting an error message when I try to run the following... The data
> is drawn from the oribatid dataset.
>
> data(oribatid)
>
> mite <- oribatid$fau
> mite.xy <- oribatid$xy
> mite.dbmem1 <- dbmem(mite.xy, thresh=1.012, MEM.autocor = "non-null",
> silent = FALSE)
> s.label(mite.xy, nb = attr(mite.dbmem1, "listw"))
>
> Error in s.label(mite.xy, nb = attr(mite.dbmem1, "listw")) :
>  unused argument (nb = attr(mite.dbmem1, "listw"))
> I dont know what the nb argument is here?
>
> # Plot maps of the first 3 dbMEM eigenfunctions
> s.value(mite.xy, mite.dbmem1[,1:3])
>
> Error in s.value(mite.xy, mite.dbmem1[, 1:3]) :
>  Non equal row numbers 70 3
>
>
> I checked the mite.xy and mite.dbmem1 data and they both have 70 rows?
>
> Andy
>
>
>
> --
> Andrew Halford Ph.D
> Research Scientist (Kimberley Marine Parks)
> Dept. Parks and Wildlife
> Western Australia
>
> Ph: +61 8 9219 9795 <+61%208%209219%209795>
> Mobile: +61 (0) 468 419 473 <+61%20468%20419%20473>
>
>
>
> --
> Andrew Halford Ph.D
> Research Scientist (Kimberley Marine Parks)
> Dept. Parks and Wildlife
> Western Australia
>
> Ph: +61 8 9219 9795
> Mobile: +61 (0) 468 419 473
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

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