## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(message = FALSE, warning = FALSE)

## ----echo=TRUE,eval=TRUE,results='hide'---------------------------------------
library(spdep)
if (require(rgdal, quietly=TRUE)) {
  eire <- readOGR(system.file("shapes/eire.shp", package="spData")[1])
} else {
  require(maptools, quietly=TRUE)
  eire <- readShapeSpatial(system.file("shapes/eire.shp", package="spData")[1])
}
row.names(eire) <- as.character(eire$names)
proj4string(eire) <- CRS("+proj=utm +zone=30 +ellps=airy +units=km")

## ----echo=TRUE,eval=TRUE------------------------------------------------------
class(eire)
names(eire)

## ----echo=TRUE,eval=TRUE------------------------------------------------------
fn <- system.file("etc/misc/geary_eire.txt", package="spdep")[1]
ge <- read.table(fn, header=TRUE)
names(ge)

## ----echo=TRUE,eval=TRUE------------------------------------------------------
row.names(ge) <- as.character(ge$county)
all.equal(row.names(ge), row.names(eire))
library(maptools)
eire_ge <- spCbind(eire, ge)

## ----echo=TRUE,eval=TRUE------------------------------------------------------
eire_ge1 <- eire_ge[!(row.names(eire_ge) %in% "Dublin"),]
length(row.names(eire_ge1))

## ----echo=TRUE,eval=TRUE------------------------------------------------------
skewness <- function(z) {z <- scale(z, scale=FALSE); ((sum(z^3)/length(z))^2)/((sum(z^2)/length(z))^3)}
kurtosis <- function(z) {z <- scale(z, scale=FALSE); (sum(z^4)/length(z))/((sum(z^2)/length(z))^2)}

## ----echo=TRUE,eval=TRUE------------------------------------------------------
print(sapply(as(eire_ge1, "data.frame")[13:24], skewness), digits=3)
print(sapply(as(eire_ge1, "data.frame")[13:24], kurtosis), digits=4)
print(sapply(as(eire_ge1, "data.frame")[c(13,16,18,19)], function(x) skewness(log(x))), digits=3)
print(sapply(as(eire_ge1, "data.frame")[c(13,16,18,19)], function(x) kurtosis(log(x))), digits=4)

## ----echo=TRUE,eval=TRUE------------------------------------------------------
fn <- system.file("etc/misc/unstand_sn.txt", package="spdep")[1]
unstand <- read.table(fn, header=TRUE)
summary(unstand)

## ----echo=TRUE,eval=TRUE------------------------------------------------------
class(unstand) <- c("spatial.neighbour", class(unstand))
of <- ordered(unstand$from)
attr(unstand, "region.id") <- levels(of)
unstand$from <- as.integer(of)
unstand$to <- as.integer(ordered(unstand$to))
attr(unstand, "n") <- length(unique(unstand$from))

## ----echo=TRUE,eval=TRUE------------------------------------------------------
lw_unstand <- sn2listw(unstand)
lw_unstand$style <- "B"
lw_unstand

## ----echo=TRUE,eval=TRUE------------------------------------------------------
nb <- poly2nb(eire_ge1)
nb

## ----echo=TRUE,eval=TRUE------------------------------------------------------
xx <- diffnb(nb, lw_unstand$neighbours, verbose=TRUE)

## ----echo=TRUE,eval=FALSE,results='hide'--------------------------------------
#  plot(eire_ge1, border="grey60")
#  plot(nb, coordinates(eire_ge1), add=TRUE, pch=".", lwd=2)
#  plot(xx, coordinates(eire_ge1), add=TRUE, pch=".", lwd=2, col=3)

## ----eval=TRUE,echo=FALSE, fig.cap="County boundaries and contiguities"-------
par(mfrow=c(1,2))
plot(eire_ge1, border="grey40")
title(xlab="25 Irish counties")
text(coordinates(eire_ge1), labels=as.character(eire_ge1$serlet), cex=0.8)
plot(eire_ge1, border="grey60")
title(xlab="Contiguities")
plot(nb, coordinates(eire_ge1), add=TRUE, pch=".", lwd=2)
plot(xx, coordinates(eire_ge1), add=TRUE, pch=".", lwd=2, col=3)
legend("topleft", legend=c("Contiguous", "Ferry"), lwd=2, lty=1, col=c(1,3), bty="n", cex=0.7)
par(mfrow=c(1,1))

## ----echo=FALSE,eval=TRUE-----------------------------------------------------
load(system.file("etc/misc/raw_grass_borders.RData", package="spdep")[1])

## ----echo=TRUE,eval=FALSE,results='hide'--------------------------------------
#  library(maptools)
#  SG <- Sobj_SpatialGrid(eire_ge1)$SG
#  library(spgrass6)
#  grass_home <- "/home/rsb/topics/grass/g64/grass-6.4.0svn"
#  initGRASS(grass_home, home=tempdir(), SG=SG, override=TRUE)
#  writeVECT6(eire_ge1, "eire", v.in.ogr_flags=c("o", "overwrite"))
#  res <- vect2neigh("eire", ID="serlet")

## ----echo=TRUE,eval=TRUE------------------------------------------------------
grass_borders <- sn2listw(res)
raw_borders <- grass_borders$weights
int_tot <- attr(res, "total") - attr(res, "external")
prop_borders <- lapply(1:length(int_tot), function(i) raw_borders[[i]]/int_tot[i])
dlist <- nbdists(grass_borders$neighbours, coordinates(eire_ge1))
inv_dlist <- lapply(dlist, function(x) 1/(x/1.609344))
combo_km <- lapply(1:length(inv_dlist), function(i) inv_dlist[[i]]*prop_borders[[i]])
combo_km_lw <- nb2listw(grass_borders$neighbours, glist=combo_km, style="B")
summary(combo_km_lw)

## ----echo=TRUE,eval=TRUE------------------------------------------------------
red_lw_unstand <- lw_unstand
Clare <- which(attr(lw_unstand, "region.id") == "C")
Kerry <- which(attr(lw_unstand, "region.id") == "H")
Kerry_in_Clare <- which(lw_unstand$neighbours[[Clare]] == Kerry)
Clare_in_Kerry <- which(lw_unstand$neighbours[[Kerry]] == Clare)
red_lw_unstand$neighbours[[Clare]] <- red_lw_unstand$neighbours[[Clare]][-Kerry_in_Clare]
red_lw_unstand$neighbours[[Kerry]] <- red_lw_unstand$neighbours[[Kerry]][-Clare_in_Kerry]
red_lw_unstand$weights[[Clare]] <- red_lw_unstand$weights[[Clare]][-Kerry_in_Clare]
red_lw_unstand$weights[[Kerry]] <- red_lw_unstand$weights[[Kerry]][-Clare_in_Kerry]
summary(red_lw_unstand)
cor(unlist(red_lw_unstand$weights), unlist(combo_km_lw$weights))

## ----echo=TRUE,eval=TRUE------------------------------------------------------
flatten <- function(x, digits=3, statistic="I") {
  res <- c(format(x$estimate, digits=digits),
    format(x$statistic, digits=digits),
    format.pval(x$p.value, digits=digits))
  res <- matrix(res, ncol=length(res))
  colnames(res) <- paste(c("", "E", "V", "SD_", "P_"), "I", sep="")
  rownames(res) <- deparse(substitute(x))
  res
}
`reconstructed weights` <- moran.test(eire_ge1$ocattlepacre, combo_km_lw)
`original weights` <- moran.test(eire_ge1$ocattlepacre, red_lw_unstand)
print(rbind(flatten(`reconstructed weights`), flatten(`original weights`)), quote=FALSE)

## ----echo=TRUE,eval=TRUE------------------------------------------------------
eire_ge1$ln_pagval2_10 <- log(eire_ge1$pagval2_10)
eire_ge1$ln_cowspacre <- log(eire_ge1$cowspacre)
eire_ge1$ln_pigspacre <- log(eire_ge1$pigspacre)
eire_ge1$ln_sheeppacre <- log(eire_ge1$sheeppacre)
vars <- c("pagval2_10", "ln_pagval2_10", "pagval10_50", "pagval50p",
 "cowspacre", "ln_cowspacre", "ocattlepacre", "pigspacre",
 "ln_pigspacre", "sheeppacre", "ln_sheeppacre", "townvillp",
 "carspcap", "radiopcap", "retailpcap", "psinglem30_34")
nb_B <- nb2listw(lw_unstand$neighbours, style="B")
nb_B
lw_std <- nb2listw(lw_unstand$neighbours, glist=lw_unstand$weights, style="W")
lw_std

## ----echo=TRUE,eval=TRUE------------------------------------------------------
system.time({
MoranN <- lapply(vars, function(x) moran.test(eire_ge1[[x]], listw=nb_B, randomisation=FALSE))
MoranR <- lapply(vars, function(x) moran.test(eire_ge1[[x]], listw=nb_B, randomisation=TRUE))
GearyN <- lapply(vars, function(x) geary.test(eire_ge1[[x]], listw=nb_B, randomisation=FALSE))
GearyR <- lapply(vars, function(x) geary.test(eire_ge1[[x]], listw=nb_B, randomisation=TRUE))
Prop_unstdN  <- lapply(vars, function(x) moran.test(eire_ge1[[x]], listw=lw_unstand, randomisation=FALSE))
Prop_unstdR  <- lapply(vars, function(x) moran.test(eire_ge1[[x]], listw=lw_unstand, randomisation=TRUE))
Prop_stdN  <- lapply(vars, function(x) moran.test(eire_ge1[[x]], listw=lw_std, randomisation=FALSE))
Prop_stdR  <- lapply(vars, function(x) moran.test(eire_ge1[[x]], listw=lw_std, randomisation=TRUE))
})
res <- sapply(c("MoranN", "MoranR", "GearyN", "GearyR", "Prop_unstdN", "Prop_unstdR", "Prop_stdN", "Prop_stdR"), function(x) sapply(get(x), "[[", "statistic"))
rownames(res) <- vars
ores <- res[,c(1,2,5:8)]

## ----echo=FALSE,eval=TRUE-------------------------------------------------------------------------
options("width"=100)

## ----echo=TRUE,eval=TRUE--------------------------------------------------------------------------
print(formatC(res, format="f", digits=4), quote=FALSE)

## ----echo=FALSE,eval=TRUE---------------------------------------------------------------
options("width"=90)

## ----echo=TRUE,eval=TRUE----------------------------------------------------------------
wc_unstd <- spweights.constants(lw_unstand)
wrong_N_sqVI <- sqrt((wc_unstd$nn*wc_unstd$S1 - wc_unstd$n*wc_unstd$S2 + 3*wc_unstd$S0*wc_unstd$S0)/((wc_unstd$nn-1)*wc_unstd$S0*wc_unstd$S0)-((-1/(wc_unstd$n-1))^2))
raw_data <- grep("^ln_", vars, invert=TRUE)
I <- sapply(Prop_stdN, function(x) x$estimate[1])[raw_data]
EI <- sapply(Prop_stdN, function(x) x$estimate[2])[raw_data]
res <- (I - EI)/wrong_N_sqVI
names(res) <- vars[raw_data]
print(formatC(res, format="f", digits=4), quote=FALSE)

## ----echo=TRUE,eval=TRUE----------------------------------------------------------------
res <- lapply(c("MoranR", "GearyR", "Prop_unstdR", "Prop_stdR"), function(x) sapply(get(x), function(y) c(y$estimate[1], sqrt(y$estimate[3]))))
res <- t(do.call("rbind", res))
colnames(res) <- c("I", "sigma_I", "C", "sigma_C", "unstd_r", "sigma_r", "std_r", "sigma_r")
rownames(res) <- vars
print(formatC(res, format="f", digits=4), quote=FALSE)

## ----echo=TRUE,eval=TRUE----------------------------------------------------------------
oMoranf <- function(x, nb) {
  z <- scale(x, scale=FALSE)
  n <- length(z)
  glist <- lapply(1:n, function(i) {ii <- nb[[i]]; ifelse(ii > i, 1, 0)})
  lw <- nb2listw(nb, glist=glist, style="B")
  wz <- lag(lw, z)
  I <- (sum(z*wz)/sum(z*z))
  I
}
res <- sapply(vars, function(x) oMoranf(eire_ge1[[x]], nb=lw_unstand$neighbours))
print(formatC(res, format="f", digits=4), quote=FALSE)

## ----echo=TRUE,eval=TRUE----------------------------------------------------------------
MoranI.boot <- function(var, i, ...) {
  var <- var[i]
  return(moran(x=var, ...)$I)
}
Nsim <- function(d, mle) {
  n <- length(d)
  rnorm(n, mle$mean, mle$sd)
}
f_bperm <- function(x, nsim, listw) {
  boot(x, statistic=MoranI.boot, R=nsim, sim="permutation", listw=listw,
    n=length(x), S0=Szero(listw))
}
f_bpara <- function(x, nsim, listw) {
  boot(x, statistic=MoranI.boot, R=nsim, sim="parametric", ran.gen=Nsim,
    mle=list(mean=mean(x), sd=sd(x)), listw=listw, n=length(x),
    S0=Szero(listw))
}
nsim <- 4999
set.seed(1234)

## ----echo=TRUE,eval=FALSE---------------------------------------------------------------
#  system.time({
#  MoranNb <- lapply(vars, function(x) f_bpara(x=eire_ge1[[x]], nsim=nsim, listw=nb_B))
#  MoranRb <- lapply(vars, function(x) f_bperm(x=eire_ge1[[x]], nsim=nsim, listw=nb_B))
#  Prop_unstdNb  <- lapply(vars, function(x) f_bpara(x=eire_ge1[[x]], nsim=nsim, listw=lw_unstand))
#  Prop_unstdRb  <- lapply(vars, function(x) f_bperm(x=eire_ge1[[x]], nsim=nsim, listw=lw_unstand))
#  Prop_stdNb  <- lapply(vars, function(x) f_bpara(x=eire_ge1[[x]], nsim=nsim, listw=lw_std))
#  Prop_stdRb  <- lapply(vars, function(x) f_bperm(x=eire_ge1[[x]], nsim=nsim, listw=lw_std))
#  })

## ----echo=FALSE,eval=FALSE--------------------------------------------------------------
#  zzz <- system.time({
#  MoranNb <- lapply(vars, function(x) f_bpara(x=eire_ge1[[x]], nsim=nsim, listw=nb_B))
#  MoranRb <- lapply(vars, function(x) f_bperm(x=eire_ge1[[x]], nsim=nsim, listw=nb_B))
#  Prop_unstdNb  <- lapply(vars, function(x) f_bpara(x=eire_ge1[[x]], nsim=nsim, listw=lw_unstand))
#  Prop_unstdRb  <- lapply(vars, function(x) f_bperm(x=eire_ge1[[x]], nsim=nsim, listw=lw_unstand))
#  Prop_stdNb  <- lapply(vars, function(x) f_bpara(x=eire_ge1[[x]], nsim=nsim, listw=lw_std))
#  Prop_stdRb  <- lapply(vars, function(x) f_bperm(x=eire_ge1[[x]], nsim=nsim, listw=lw_std))
#  })
#  res <- lapply(c("MoranNb", "MoranRb", "Prop_unstdNb", "Prop_unstdRb", "Prop_stdNb", "Prop_stdRb"), function(x) sapply(get(x), function(y) (y$t0 - mean(y$t))/sd(y$t)))
#  res <- t(do.call("rbind", res))
#  colnames(res) <- c("MoranNb", "MoranRb", "Prop_unstdNb", "Prop_unstdRb", "Prop_stdNb", "Prop_stdRb")
#  rownames(res) <- vars
#  save(zzz, res, file="backstore/boot_res.RData")

## ----echo=FALSE,eval=FALSE--------------------------------------------------------------
#  bsfn <- system.file("etc/backstore/boot_res.RData", package="spdep")
#  load(bsfn)
#  zzz

## ----echo=TRUE,eval=FALSE---------------------------------------------------------------
#  res <- lapply(c("MoranNb", "MoranRb", "Prop_unstdNb", "Prop_unstdRb", "Prop_stdNb", "Prop_stdRb"), function(x) sapply(get(x), function(y) (y$t0 - mean(y$t))/sd(y$t)))
#  res <- t(do.call("rbind", res))
#  colnames(res) <- c("MoranNb", "MoranRb", "Prop_unstdNb", "Prop_unstdRb", "Prop_stdNb", "Prop_stdRb")
#  rownames(res) <- vars

## ----echo=TRUE,eval=TRUE----------------------------------------------------------------
print(formatC(res, format="f", digits=4), quote=FALSE)
oores <- ores - res
apply(oores, 2, mad)
alpha_0.05 <- qnorm(0.05, lower.tail=FALSE)
all((res >= alpha_0.05) == (ores >= alpha_0.05))

## ----echo=TRUE,eval=TRUE----------------------------------------------------------------
lm_objs <- lapply(vars, function(x) lm(formula(paste(x, "~1")), data=eire_ge1))
system.time({
MoranSad <- lapply(lm_objs, function(x) lm.morantest.sad(x, listw=nb_B))
Prop_unstdSad  <- lapply(lm_objs, function(x) lm.morantest.sad(x, listw=lw_unstand))
Prop_stdSad  <- lapply(lm_objs, function(x) lm.morantest.sad(x, listw=lw_std))
})
res <- sapply(c("MoranSad", "Prop_unstdSad", "Prop_stdSad"), function(x) sapply(get(x), "[[", "statistic"))
rownames(res) <- vars

## ----echo=TRUE,eval=TRUE----------------------------------------------------------------
print(formatC(res, format="f", digits=4), quote=FALSE)
oores <- res - ores[,c(1,3,5)]
apply(oores, 2, mad)
all((res >= alpha_0.05) == (ores[,c(1,3,5)] >= alpha_0.05))

## ----echo=TRUE,eval=TRUE----------------------------------------------------------------
system.time({ 
MoranEx <- lapply(lm_objs, function(x) lm.morantest.exact(x, listw=nb_B))
Prop_unstdEx  <- lapply(lm_objs, function(x) lm.morantest.exact(x, listw=lw_unstand))
Prop_stdEx  <- lapply(lm_objs, function(x) lm.morantest.exact(x, listw=lw_std))
})
res <- sapply(c("MoranEx", "Prop_unstdEx", "Prop_stdEx"), function(x) sapply(get(x), "[[", "statistic"))
rownames(res) <- vars

## ----echo=TRUE,eval=TRUE----------------------------------------------------------------
print(formatC(res, format="f", digits=4), quote=FALSE)
oores <- res - ores[,c(1,3,5)]
apply(oores, 2, mad)
all((res >= alpha_0.05) == (ores[,c(1,3,5)] >= alpha_0.05))

## ---- echo=FALSE,eval=TRUE--------------------------------------------------------------
run <- require("spatialreg", quiet=TRUE) && packageVersion("spatialreg") >= "1.2"

## ----echo=TRUE,eval=run-----------------------------------------------------------------
vars_scaled <- lapply(vars, function(x) scale(eire_ge1[[x]], scale=FALSE))
nb_W <- nb2listw(lw_unstand$neighbours, style="W")
pre <- spatialreg:::preAple(0, listw=nb_W)
MoranAPLE <- sapply(vars_scaled, function(x) spatialreg:::inAple(x, pre))
pre <- spatialreg:::preAple(0, listw=lw_std, override_similarity_check=TRUE)
Prop_stdAPLE <- sapply(vars_scaled, function(x) spatialreg:::inAple(x, pre))
res <- cbind(MoranAPLE, Prop_stdAPLE)
colnames(res) <- c("APLE W", "APLE Gstd")
rownames(res) <- vars

## ----echo=TRUE,eval=run-----------------------------------------------------------------
print(formatC(res, format="f", digits=4), quote=FALSE)

## ----results='asis',eval=TRUE,echo=FALSE, fig.cap="Three contrasted spatial weights definitions"----
pal <- grey.colors(9, 1, 0.5, 2.2)
oopar <- par(mfrow=c(1,3), mar=c(1,1,3,1)+0.1)
z <- t(listw2mat(nb_B))
brks <- c(0,0.1,1)
image(1:25, 1:25, z[,ncol(z):1], breaks=brks, col=pal[c(1,9)],
 main="Binary", axes=FALSE)
box()
z <- t(listw2mat(lw_unstand))
brks <- c(0,quantile(c(z)[c(z) > 0], seq(0,1,1/8)))
image(1:25, 1:25, z[,ncol(z):1], breaks=brks, col=pal, main="General", axes=FALSE)
box()
z <- t(listw2mat(lw_std))
brks <- c(0,quantile(c(z)[c(z) > 0], seq(0,1,1/8)))
image(1:25, 1:25, z[,ncol(z):1], breaks=brks, col=pal,
 main="Std. general", axes=FALSE)
box()
par(oopar)

## ----results='asis',eval=TRUE,echo=FALSE------------------------------------------------
eire_ge1$nb_B <- sapply(nb_B$weights, sum)
eire_ge1$lw_unstand <- sapply(lw_unstand$weights, sum)
library(lattice)
trellis.par.set(sp.theme())
p1 <- spplot(eire_ge1, c("nb_B"), main="Binary")
p2 <- spplot(eire_ge1, c("lw_unstand"), main="General")
print(p1, split=c(1,1,2,1), more=TRUE)
print(p2, split=c(2,1,2,1), more=FALSE)

