[R-sig-Geo] editing a correlogram
Leonardo Matheus Servino
|eon@rdom@erv|no @end|ng |rom gm@||@com
Sun Mar 17 21:07:41 CET 2019
My script:
library(spdep)
setwd('C:/Dados')
dados_I_langsdorffii<-read.csv('I_langsdorffii.csv', sep=';')
coords<-cbind(dados_I_langsdorffii$LONG, dados_I_langsdorffii$LAT)
coords1<-as.matrix(coords)
source("plot.links.r")
plot.links(coords, thresh = 0.5, text = F)
vizinho<-dnearneigh(as.matrix(coords1), 0, 0.5)
summary(vizinho)
corre.sp <- sp.correlogram(vizinho, dados_I_langsdorffii$MEDIANA_CRC, order
=5, method = "I",zero.policy = TRUE)
print(corre.sp, p.adj.method = "holm")
par(adj="0.5",family="serif",cex.axis="1.5",xaxs="r",cex.axis="2.5",cex.lab="2.5",las="1",tcl="-0.25",lwd="1.8",
ps="5", mex="0.7", lty="blank")
plot(corre.sp, p.adj.method = "holm", main="",ylim=c(-1,1))
Em sáb, 16 de mar de 2019 às 19:04, Roger Bivand <Roger.Bivand using nhh.no>
escreveu:
> On Sat, 16 Mar 2019, Ben Tupper wrote:
>
> > Hi,
> >
> > In this case the spdep::plot.spcor() function, which I think you are
> > using, doesn't provide the mechanism for the caller to override the
> > default pch value. You can see this by looking at the pl.spcor function
> > (as shown way below.) I think it may be easiest for you to simply
> > rewrite the function with the plotting parameters assigned as arguments.
>
> Thanks, indeed the ... should be passed through to plotting functions,
> and I'll look at doing this. My preference would be to extract the
> components of the returned object needed for customised plotting, not
> trying to finesse the plot method, which was always meant for guidance,
> like other diagnostic plots.
>
> As Rolf said, an example of the code you are using (on a built-in data
> set) to show what you want would make things easier, say based on the help
> page example. Note that print method returns its calculations invisibly
> too.
>
> nc.sids <- st_read(system.file("shapes/sids.shp", package="spData")[1],
> quiet=TRUE)
> rn <- as.character(nc.sids$FIPS)
> ncCC89_nb <- read.gal(system.file("weights/ncCC89.gal",
> package="spData")[1],
> region.id=rn)
> ft.SID74 <- sqrt(1000)*(sqrt(nc.sids$SID74/nc.sids$BIR74) +
> sqrt((nc.sids$SID74+1)/nc.sids$BIR74))
> tr.SIDS74 <- ft.SID74*sqrt(nc.sids$BIR74)
> Ispc <- sp.correlogram(ncCC89_nb, tr.SIDS74, order=8, method="I",
> zero.policy=TRUE)
> str(Ispc)
> str(print(Ispc, "bonferroni"))
> Ispc_b <- as.data.frame(print(Ispc, "bonferroni"))
> Ispc_b$lag <- 1:8
> library(ggplot2)
> ggplot(Ispc_b) + geom_point(aes(x=lag, y=estimate))
> + geom_hline(yintercept=0)
>
> Or whatever you feel like doing.
>
> Roger
>
> >
> > Cheers,
> > Ben
> >
> >
> >> spdep::plot.spcor
> > function (x, main, ylab, ylim, ...)
> > {
> > if (missing(main))
> > main <- x$var
> > if ((x$method == "I") || (x$method == "C")) {
> > lags <- as.integer(rownames(x$res))
> > to.plot <- which((x$res[, 3] > 0) & (x$res[, 3] != Inf))
> > sd2 <- rep(0, nrow(x$res))
> > sd2[to.plot] <- 2 * sqrt(x$res[to.plot, 3])
> > if (missing(ylim)) {
> > ylim <- range(c(x$res[, 1] + sd2, x$res[, 1] - sd2))
> > }
> > if (missing(ylab))
> > if (x$method == "I")
> > ylab <- "Moran's I"
> > if (x$method == "C")
> > ylab <- "Geary's C"
> > plot(lags, x$res[, 1], type = "p", pch = 18, ylim = ylim,
> > main = main, ylab = ylab, xaxt = "n")
> > arrows(lags, x$res[, 1] + sd2, lags, x$res[, 1] - sd2,
> > length = 0.1, angle = 90)
> > arrows(lags, x$res[, 1] - sd2, lags, x$res[, 1] + sd2,
> > length = 0.1, angle = 90)
> > axis(1, at = lags)
> > abline(h = x$res[1, 2])
> > }
> > else {
> > res <- as.vector(x$res)
> > lags <- as.integer(names(x$res))
> > if (missing(ylim))
> > ylim <- c(-1, 1)
> > if (missing(ylab))
> > ylab <- "Spatial autocorrelation"
> > plot(lags, res, type = "h", ylim = ylim, main = main,
> > ylab = ylab, lwd = 4, xaxt = "n")
> > axis(1, at = lags)
> > abline(h = 0)
> > }
> > }
> > <bytecode: 0x7fb8799d0e40>
> > <environment: namespace:spdep>
> >
> >
> >
> >> On Mar 16, 2019, at 1:16 PM, Leonardo Matheus Servino <
> leonardomservino using gmail.com> wrote:
> >>
> >> I tried the function par() and arguments inside the plot(), but some
> >> parameters doesn't change.
> >> For example, the argument pch=, which changes the symbols that
> represents
> >> the points in the plot doesn't work.
> >>
> >>
> >> Em sáb, 16 de mar de 2019 às 13:48, Sarah Goslee <
> sarah.goslee using gmail.com <mailto:sarah.goslee using gmail.com>>
> >> escreveu:
> >>
> >>> Of course.
> >>>
> >>> The ... argument to the plot method means that you can use standard
> >>> base graphics options to customize as you wish.
> >>>
> >>> ?par gives the whole list, although they may not all be useful for
> >>> correlograms.
> >>>
> >>> If you have specific questions after you try customizing to your
> >>> liking, the list can certainly help with details.
> >>>
> >>> Sarah
> >>>
> >>> On Sat, Mar 16, 2019 at 11:00 AM Leonardo Matheus Servino
> >>> <leonardomservino using gmail.com> wrote:
> >>>>
> >>>> Hello,
> >>>>
> >>>> I've been tried to use the function "sp.correlogram". After plot the
> >>>> correlogram, I would like to edit the grafic's appearence, to publish
> it.
> >>>> It is possible?
> >>>>
> >>>> Thanks
> >>>>
> >>>> --
> >>>> Leonardo Matheus Servino
> >>>> Pós-Graduação em Evolução e Diversidade
> >>>> Universidade Federal do ABC - UFABC - Centro de Ciências Naturais e
> >>> Humanas
> >>>>
> >>>
> >>> --
> >>> Sarah Goslee (she/her)
> >>> http://www.numberwright.com
> >>>
> >>
> >>
> >> --
> >> Leonardo Matheus Servino
> >> Pós-Graduação em Evolução e Diversidade
> >> Universidade Federal do ABC - UFABC - Centro de Ciências Naturais e
> Humanas
> >>
> >> LED I - Laboratório de Evolução e Diversidade I - Bloco Delta, sala 202
> >>
> >> Rua Arcturus, 3. Jardim Antares
> >> 09606-070 São Bernardo do Campo - SP
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> R-sig-Geo using r-project.org <mailto:R-sig-Geo using r-project.org>
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo <
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo>
> > Ben Tupper
> > Bigelow Laboratory for Ocean Sciences
> > 60 Bigelow Drive, P.O. Box 380
> > East Boothbay, Maine 04544
> > http://www.bigelow.org
> >
> > Ecological Forecasting: https://eco.bigelow.org/
> >
> >
> >
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo using 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; e-mail: Roger.Bivand using nhh.no
> https://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
--
Leonardo Matheus Servino
Pós-Graduação em Evolução e Diversidade
Universidade Federal do ABC - UFABC - Centro de Ciências Naturais e Humanas
LED I - Laboratório de Evolução e Diversidade I - Bloco Delta, sala 202
Rua Arcturus, 3. Jardim Antares
09606-070 São Bernardo do Campo - SP
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