Poisson regression spatial residual plot
On 01/09/2013 10:07 PM, Milan Sharma wrote:
Dear all,? I want to plot Poisson regression spatial residual plot, all the codes run but there is a small error? at the end in spplot command, which is shown below. Can someone figure out what is wrong? ##################################
GLMp <- glm(Tcrash~X100MVMT+Alcohol+Alignment+PVMT+offset(log(population)), data=data, family="poisson") summary(GLMp)
Call: glm(formula = Tcrash ~ X100MVMT + Alcohol + Alignment + PVMT + ? ? ? offset(log(population)), family = "poisson", data = data) Deviance Residuals: ? ? ? Min? ? ? ? ? ? 1Q? ? Median? ? ? ? ? ? 3Q? ? ? ? ? Max ? -19.144? ? -3.900? ? -0.500? ? ? 2.693? ? 24.990 ? Coefficients: ? ? ? ? ? ? ? ? ? ? ? ? ? Estimate Std. Error z value Pr(>|z|)? ? ? (Intercept) -4.456e+00? 4.740e-02 -94.012? < 2e-16 *** X100MVMT? ? ? -5.574e-05? 2.457e-06 -22.688? < 2e-16 *** Alcohol? ? ? ? -2.378e+00? 2.598e-01? -9.153? < 2e-16 *** Alignment? ? ? 2.872e-01? 7.207e-02? ? 3.985 6.75e-05 *** PVMT? ? ? ? ? ? ? ? 7.467e-01? 1.197e-01? ? 6.236 4.48e-10 *** --- Signif. codes:? 0 ???***??? 0.001 ???**??? 0.01 ???*??? 0.05 ???.??? 0.1 ??? ??? 1 (Dispersion parameter for poisson family taken to be 1) ? ? ? Null deviance: 5089.2? on 70? degrees of freedom Residual deviance: 3736.1? on 66? degrees of freedom AIC: 4325.1 Number of Fisher Scoring iterations: 4
lmpresid <- residuals(GLMp, type="deviance") #Display residuals; REMOVE sp.layout=list(TCEpts) spplot(data, "lmpresid",col.regions=grey.colors(9, 0.95, 0.55, 2.2), at=seq(-3,5,length.out=9))
Error in function (classes, fdef, mtable)? : ? unable to find an inherited method for function "spplot", for signature "data.frame"
Milan
Milan, your email is unreadable and your script is unreproducible. the error says that object data (which I don't see created in your script) is of class data.frame -- spplot needs Spatial* objects to do something useful.
________________________________
From: Virgilio G??mez-Rubio <virgilio.gomez at uclm.es>
Cc: "r-sig-geo at r-project.org" <r-sig-geo at r-project.org>
Sent: Tuesday, January 8, 2013 1:42 PM
Subject: Re: [R-sig-Geo] Poisson regression spatial residual plot
Dear Milan,
El mar, 08-01-2013 a las 06:48 -0800, Milan Sharma escribi??:
Dear list,
I wanted to plot residuals from poisson regression model (like the figure 10.5 of Applied spatial data analysis with R, Bivand et. al.).
My data has response,Tcrash, and the covariates,
100MVMT, Alcohol PVMT Alignment
and longitude and latitude.
I used their code, but what "TCE" represents in my case, I am unable to figure out.
TCE refers to a number of sites and they are just another layer on the
plot but has nothing to do on the GLM.
I will paste a small portion of data and code here, if that helps.
Please, help me, if possible.
wi<-map("county", "wisconsin", fill=TRUE, plot=FALSE)
county.names<-as.character(wi$names)
wi.sp<-map2SpatialPolygons(wi, IDs=county.names, proj4string=CRS("+proj=longlat"))
WI_queen<-poly2nb(wi.sp,
queen=TRUE)
WI_queenb<-nb2listw(WI_queen, style="B")
summary(WI_queenb)
WI_queenw<-nb2listw(WI_queen, style="W")
County population Tcrash 100MVMT Alcohol PVMT Alignment Longitude Latitude
adams 18643 225 225.6 0.093333 0.288889 0.155556 -89.792 43.95184
ashland 16866 187 174.3 0.058824 0.368984 0.235294 -90.7791 46.46137
barron 44963 379 495.5 0.055409 0.358839 0.248021 -91.821 45.43696
The R code in lat2.R (available from www.asdar-book.org) that need to
look at are:
#Fit GLM
nyGLMp <- glm(Cases~PEXPOSURE+PCTAGE65P+PCTOWNHOME+offset(log(POP8)),
data=NY8, family="poisson")
#Get residuals
NY8$lmpresid <- residuals(nyGLMp, type="deviance")
#Display residuals; REMOVE sp.layout=list(TCEpts)
spplot(NY8, "lmpresid", sp.layout=list(TCEpts),
col.regions=grey.colors(9, 0.95, 0.55, 2.2),
at=seq(-3,5,length.out=9))
You will need to change the names of the variables in the model but you
should be able to plot the residuals by customizing these tree lines of
code.
Best,
Virgilio
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