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List: r-sig-geo
Subject: Re: [R-sig-Geo] spdep: new zero.policy attribute
From: Roger Bivand <Roger.Bivand () nhh ! no>
Date: 2023-11-09 11:52:24
Message-ID: SV0P279MB0475000B80A52A2CE8A8A2FFEEAFA () SV0P279MB0475 ! NORP279 ! PROD ! OUTLOOK ! COM
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Thanks, Josiah and Connor!
We are moving the discussion to: https://github.com/gpiras/sphet/issues/17 for those \
who can participate there - if someone with comments prefers not to write there, \
please continue to follow up here.
Roger
--
Roger Bivand
Emeritus Professor
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
Roger.Bivand@nhh.no
________________________________________
From: Josiah Parry <josiah.parry@gmail.com>
Sent: 05 November 2023 18:01
To: Roger Bivand
Cc: r-sig-geo@r-project.org
Subject: Re: [R-sig-Geo] spdep: new zero.policy attribute
You don't often get email from josiah.parry@gmail.com. Learn why this is \
important<https://aka.ms/LearnAboutSenderIdentification> My take is generally that \
less is more. In the case of an isolated node, I think the best thing to do is to \
return NA rather than 0. For example consider administrative boundaries where the \
lagged variable is median household income. If we returned a 0 in that case, we'd \
likely be introducing quite the outlier!
My preference would be to _always_ default to NA lagged values when no neighbors are \
present. Additionally, it would be quite nice to instruct users on how to impute \
these values with other lagged variables. Say we have an isolated node, but we don't \
want an NA value. We can impute that missing value with the spatial lag of the \
variable using a different neighborhood construction—e.g. using KNN with k = 3 to \
ensure that the node always has values to lag.
Here is an example gist imputing k=3 lag \
https://gist.github.com/JosiahParry/eb7878fc375fb931ddd6675a2c591a2b<https://eur02.saf \
elinks.protection.outlook.com/?url=https%3A%2F%2Fgist.github.com%2FJosiahParry%2Feb787 \
8fc375fb931ddd6675a2c591a2b&data=05%7C01%7CRoger.Bivand%40nhh.no%7C2486f70674ed4d8f788 \
508dbde20f09c%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638348005283188250%7CUnknow \
n%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=K8weAXIlvFdTkHIlsVnJSgTbwG%2F2GNOn57XTtu9rMpQ%3D&reserved=0>
Another option could be to use the focal feature's value as the lag itself. If a \
location has no neighborhood could we argue that the location is its own \
neighborhood?
I'm not too familiar with the models to comment on them, though. I do see this more \
as a pre-processing / data imputation issue. I suspect that's more of a machine \
learning paradigm though!
On Sun, Nov 5, 2023 at 10:31 AM Roger Bivand \
<Roger.Bivand@nhh.no<mailto:Roger.Bivand@nhh.no>> wrote: And a question: in \
nb2listw() and similar functions creating spatial weights listw objects, would it be \
sensible to guess that the presence of no-neighbour observations in the input nb \
neighbour implies the choice of a spatially lagged value of zero (zero.policy=TRUE), \
lx = Wx, rather than NA (zero.policy=FALSE)?
That is, use by default zero.policy=any(card(nb) == 0L) rather than zero.policy=NULL \
and look in the spdep option set by default on package load to FALSE but settable by \
the user?
Would this be taking trying to be helpful too far, given that the analyst is creating \
the neighbour object and presumably should take responsibility for choices made?
Context: polygons not sharing boundaries with other polygons do exist legitimately in \
data sources, but setting spatially lagged values to zero for those polygons is quite \
an invasive imputation. It may be better to oblige the user to make the choice when \
the spatial weights listw object is created.
Little is known about the problem, for a recent treatment for CAR models see: \
https://arxiv.org/abs/1705.04854<https://eur02.safelinks.protection.outlook.com/?url=h \
ttps%3A%2F%2Farxiv.org%2Fabs%2F1705.04854&data=05%7C01%7CRoger.Bivand%40nhh.no%7C2486f \
70674ed4d8f788508dbde20f09c%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C6383480052831 \
88250%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJX \
VCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GzEc02zEBhB8Y9D6Xy7To%2FX2qjCF5p9EzxeEjmVF6a8%3D&reserved=0>, \
published as https://doi.org/10.1016/j.sste.2018.04.002<https://eur02.safelinks.protec \
tion.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.sste.2018.04.002&data=05%7C0 \
1%7CRoger.Bivand%40nhh.no%7C2486f70674ed4d8f788508dbde20f09c%7C33a15b2f849941998d56f20 \
b5aa91af2%7C0%7C0%7C638348005283188250%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJ \
QIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=i9DpuNPqlxtc%2ByPoiR2dUAV4uCRo33La9TxYVqAg838%3D&reserved=0>, \
where: "The specification of a CAR model on a disconnected graph is undefined ... \
[t]here are essentially two types of disconnected graphs: first, a graph containing \
an island (a singleton node with no neighbours), second, a graph split in different \
sub-graphs (each of them being a connected graph)".
This question concerns the former, singleton, case, but adding sub-graph counts if \
greater than unity to summary.nb and print.nb address the second . Very possibly, \
functions creating nb neighbour objects should themselves report that an output \
object (graph) is not connected, bigDM CARBayes CARBayesST geostan spatialreg stampr \
do call spdep::n.comp.nb themselves to check the subgraph count.
Interested in feedback,
Roger
--
Roger Bivand
Emeritus Professor
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
Roger.Bivand@nhh.no<mailto:Roger.Bivand@nhh.no>
________________________________________
From: R-sig-Geo <r-sig-geo-bounces@r-project.org<mailto:r-sig-geo-bounces@r-project.org>> \
on behalf of Roger Bivand \
<Roger.Bivand@nhh.no<mailto:Roger.Bivand@nhh.no>>
Sent: 04 November 2023 18:53
To: r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org>
Subject: [R-sig-Geo] spdep: new zero.policy attribute
In forthcoming spdep 1.3-1, spatial weight listw objects get a new zero.policy \
attribute. The attribute is added as objects are created to record the status of the \
zero.policy argument in the function creating the object, see: \
https://github.com/r-spatial/spdep/commit/e159de922c61713529a4075b0dfc2966eb8f9ad6<htt \
ps://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fr-spatial% \
2Fspdep%2Fcommit%2Fe159de922c61713529a4075b0dfc2966eb8f9ad6&data=05%7C01%7CRoger.Bivan \
d%40nhh.no%7C2486f70674ed4d8f788508dbde20f09c%7C33a15b2f849941998d56f20b5aa91af2%7C0%7 \
C0%7C638348005283188250%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLC \
JBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fZnjmNrcQKjLU3%2BDdz%2BagbRLj%2BnosBV7lapfcZwOiks%3D&reserved=0>.
Reverse dependency checks only show problems from over-eager unit testing in \
SpatialFeatureExperiment, a Bioconductor package, but other workflows may be \
impacted. The new attribute is used in tests for spatial autocorrelation to set the \
zero.policy argument in those tests (the arguments were zero.policy=NULL, are now \
zero.policy=attr(listw, "zero.policy") where listw is the spatial weights object \
argument to the test function.
This will be extended to spatialreg and friends if nobody reports negative impacts \
here soon. I'll wait before releasing 1.3-1 for a few days to see if any feedback is \
forthcoming.
Hope this long-overdue change is helpful,
Roger
--
Roger Bivand
Emeritus Professor
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
Roger.Bivand@nhh.no<mailto:Roger.Bivand@nhh.no>
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