[R-sig-Geo] A simple correlogram using sp.correlogram with data(meuse)

[Michael Treglia]

Thanks Roger! That solves it.
Best,
Mike

On Tue, Apr 28, 2015 at 12:49 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:

> On Tue, 28 Apr 2015, Michael Treglia wrote:
>
>  Hi all,
>>
>> This is a bit a tangential to the question, but related to
>> pgirmess::correlog used in this thread, so I thought it appropriate to
>> follow-up here [if not, apologies - I can start a new thread if that's
>> preferred].
>>
>> In recent exploration with the pgirmess::correlog, I was unable to change
>> the alternative hypothesis being tested. Since pgirmess::correlog uses
>> spdep::moran.test, the alternative hypothesis being tested is by default
>> "greater" (confirmed in the documentation). The help for the function
>> indicates pgirmess::correlog should also be able to take arguments from
>> 'moran.test' within it. Thus, users should be able to use the
>> 'alternative'
>> argument to change the alternative hypothesis being tested.  When trying
>> to
>> use "alternative='less'" (or 'two.sided'), an error is returned:
>>
>> Error in try(moran.test(lst.z1[[i]], nb2listw(lst.nb1[[i]], style = "W")),
>> :
>>  unused argument (alternative = "less")
>>
>
> The problem is that the ... is passed to try(), not moran.test() or
> geary.test() in:
>
> xt <- switch(pmatch(method, c("Moran", "Geary"), nomatch = 3),
>     try(moran.test(lst.z1[[i]], nb2listw(lst.nb1[[i]],
>         style = "W")), silent = TRUE, ...), try(geary.test(lst.z1[[i]],
>         nb2listw(lst.nb1[[i]], style = "W")), silent = TRUE,
>         ...), stop("Method must be 'Moran' or 'Geary'"))
>
> With:
>
> xt <- switch(pmatch(method, c("Moran", "Geary"), nomatch = 3),
>     try(moran.test(lst.z1[[i]], nb2listw(lst.nb1[[i]],
>         style = "W"), ...), silent = TRUE), try(geary.test(lst.z1[[i]],
>         nb2listw(lst.nb1[[i]], style = "W"), ...), silent = TRUE),
>         stop("Method must be 'Moran' or 'Geary'"))
>
> via for example correlog1 <- edit(correlog), it works. You can save the
> function for later use too.
>
> Hope this helps,
>
> Roger
>
>
>
>
>> Reproducible Code (based on the example from help for pgirmess::correlog):
>>
>> library(spdep)
>> library(pgirmess)
>> data(oldcol)
>> attach(COL.OLD)
>> coords<-cbind(X,Y)
>> res<-correlog(coords,CRIME, method="Moran",
>> nbclass=NULL,alternative="less")
>> ## Error in try(moran.test(lst.z1[[i]], nb2listw(lst.nb1[[i]], style =
>> "W")),  :
>> ##  unused argument (alternative = "less")
>>
>> I corresponded with the author of pgirmess and he did not have a solution
>> nor much time to work on it. I was hoping to give a go at trouble-shooting
>> myself, but haven't had a chance, so this thread seemed like a relevant
>> place to bring up the issue, so others are at least aware of it.
>>
>> Best,
>> Mike Treglia
>>
>>
>>
>>
>>
>>
>> On Tue, Apr 28, 2015 at 2:05 AM, Roger Bivand <Roger.Bivand at nhh.no>
>> wrote:
>>
>>  On Tue, 28 Apr 2015, Andy Bunn wrote:
>>>
>>>  Hi all, This seems trivial easy but being a bear of very little brain...
>>>
>>>>
>>>> I'm looking to build a correlogram using Moran's I and the function
>>>> sp.correlogram() with data(meuse) as a SpatialPointsDataFrame. I've done
>>>> so with the ncf library using correlog() but getting the equivalent out
>>>> of
>>>> library sp is eluding me. Can somebody help me out?
>>>>
>>>>
>>> require(ncf)
>>> ncf.cor <- ncf::correlog(x=coordinates(meuse)[,1],
>>>  y=coordinates(meuse)[,2], z=meuse$zinc, increment=200, resamp=100)
>>>
>>> ncf::correlog() chooses bins based on increment. Alternatively,
>>> pgirmess::correlog() uses by default an optimal number of bins, but can
>>> use
>>> a bin count:
>>>
>>> library(pgirmess)
>>> pgir.cor <- pgirmess::correlog(coordinates(meuse), z=meuse$zinc, "Moran",
>>>   nbclass=23)
>>> plot(pgir.cor[,1], pgir.cor[,2], type="b")
>>> cbind(pgir.cor[,1], ncf.cor$mean.of.class)
>>> cbind(pgir.cor[,4], ncf.cor$n)
>>>
>>> The differences come from ncf::correlog() constructing the spatial
>>> weights
>>> itself, while pgirmess::correlog() uses spdep::dnearneigh() to construct
>>> them for the distance bins and then spdep::nb2listw() and
>>> spdep::moran.test() internally in a loop, once for each bin.
>>>
>>> spdep::sp.correlogram() follows the original Cliff & Ord understanding of
>>> a spatial correlogram - like time series lags - of order 1, order 2, etc.
>>> The input spatial weights define the weighted graph, so order 2
>>> neighbours
>>> are neighbours of order 1 neighbours by stepping out on the graph.
>>> pgirmess::correlog() was written to use distance rather than graph edge
>>> count distance:
>>>
>>> library(spdep)
>>> nb200 <- dnearneigh(meuse, 0, 200)
>>> spdep.cor <- spdep::sp.correlogram(nb200, meuse$zinc, order=23,
>>>  method="I", zero.policy=TRUE)
>>> plot(spdep.cor)
>>>
>>> To get the implied mean distances for lags of nb200:
>>>
>>> nb200_23 <- nblag(nb200, 23)
>>> mdbins <- sapply(nb200_23, function(x) mean(unlist(nbdists(x, meuse))))
>>> mdbins
>>>
>>> There are two different understandings of this spatial correlogram, the
>>> C&O one based on time series and counting distance in graph edges, and
>>> another using distance bands, also found in globalG.test, etc.
>>>
>>> Hope this clarifies,
>>>
>>> Roger
>>>
>>>
>>>
>>>  -Andy
>>>>
>>>> require(sp)
>>>> require(ncf)
>>>> data(meuse)
>>>> coordinates(meuse) <- ~x+y
>>>> proj4string(meuse) <- CRS("+init=epsg:28992")
>>>> ncf.cor <- correlog(x=coordinates(meuse)[,1], y=coordinates(meuse)[,2],
>>>> z=meuse at data$zinc, increment=200, resamp=100)
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>>
>>>>  --
>>> Roger Bivand
>>> Department of Economics, Norwegian School of Economics,
>>> Helleveien 30, N-5045 Bergen, Norway.
>>> voice: +47 55 95 93 55; fax +47 55 95 91 00
>>> e-mail: Roger.Bivand at nhh.no
>>>
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> R-sig-Geo at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; fax +47 55 95 91 00
> e-mail: Roger.Bivand at nhh.no
>
>

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