View source: R/local.sp.runs.test.R
local.sp.runs.test | R Documentation |
This function calculates the local spatial runs tests for all localizations.
local.sp.runs.test(formula = NULL, data = NULL, fx = NULL,
distr = "asymptotic", listw = listw, alternative = "two.sided" , nsim = NULL,
control = list())
formula |
An (optional) formula with the factor included in |
data |
An (optional) data frame or a sf object containing the variable to testing for. |
fx |
An (optional) factor of observations with the same length as the neighbors list in |
distr |
a character string specifying the distribution "asymptotic" (default) or "bootstrap" |
listw |
A neighbourhood list (an object type knn or nb) or a W matrix that indicates the order of the elements in each $m_i-environment$ (for example of inverse distance). To calculate the number of runs in each $m_i-environment$, an order must be established, for example from the nearest neighbour to the furthest one. |
alternative |
a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less". |
nsim |
Default value is NULL to obtain the asymptotic version of the local test. For the bootstrap version nsim is the number of permutations to obtain the pseudo-value. |
control |
Optional argument. See Control Argument section. |
The object listw
can be the class:
knn
: Objects of the class knn that consider the neighbours in
order of proximity.
nb
: If the neighbours are obtained from an sf object, the code internally
will call the function nb2nb_order
it will order them in order
of proximity of the centroids.
matrix
: If a object of matrix class based in the inverse of
the distance in introduced as argument, the function nb2nb_order
will
also be called internally to transform the object the class matrix to a matrix of the
class nb with ordered neighbours.
The output is an object of the class localsrq
local.SRQ
A matrix with
runs.i | number of runs in the localization 'i'. |
E.i | expectation of local runs statistic in the localization 'i'. |
Sd.i | standard deviate of local runs statistic in the localization 'i'. |
z.value | standard value of local runs statistic (only for asymptotic version). |
p.value | p-value of local local runs statistic (only for asymptotic version). |
zseudo.value | standard value of local runs statistic (only for boots version). |
pseudo.value | p-value of local runs statistic (only for boots version). |
MeanNeig
Mean of run.i
MaxNeig
Maximum of run.i
listw
the object listw
alternative
a character string describing the alternative hypothesis
seedinit | Numerical value for the seed in boot version. Default value seedinit = 123 |
Fernando López | fernando.lopez@upct.es |
Román Mínguez | roman.minguez@uclm.es |
Antonio Páez | paezha@gmail.com |
Manuel Ruiz | manuel.ruiz@upct.es |
@references
Ruiz, M., López, F., and Páez, A. (2021). A test for global and local homogeneity of categorical data based on spatial runs. Working paper.
sp.runs.test
, dgp.spq
# Case 1: Local spatial runs test based on knn
N <- 100
cx <- runif(N)
cy <- runif(N)
x <- cbind(cx,cy)
listw <- spdep::knearneigh(cbind(cx,cy), k = 10)
p <- c(1/6,3/6,2/6)
rho <- 0.5
fx <- dgp.spq(p = p, listw = listw, rho = rho)
# Asymtotic version
lsrq <- local.sp.runs.test(fx = fx, listw = listw, alternative = "less")
print(lsrq)
plot(lsrq, sig = 0.05)
# Asymtotic version
lsrq <- local.sp.runs.test(fx = fx, listw = listw, alternative = "two.sided",
distr ="bootstrap", nsim = 399)
print(lsrq)
plot(lsrq, sig = 0.1)
# Case 2:Fastfood example. sf (points)
data("FastFood.sf")
# sf::sf_use_s2(FALSE)
x <- sf::st_coordinates(sf::st_centroid(FastFood.sf))
listw <- spdep::knearneigh(x, k = 10)
formula <- ~ Type
lsrq <- local.sp.runs.test(formula = formula, data = FastFood.sf, listw = listw)
print(lsrq)
plot(lsrq, sf = FastFood.sf, sig = 0.05)
# Case 3: With a sf object (poligons)
fname <- system.file("shape/nc.shp", package="sf")
nc <- sf::st_read(fname)
listw <- spdep::poly2nb(as(nc,"Spatial"), queen = FALSE)
p <- c(1/6,3/6,2/6)
rho = 0.5
nc$fx <- dgp.spq(p = p, listw = listw, rho = rho)
plot(nc["fx"])
formula <- ~ fx
lsrq <- local.sp.runs.test(formula = formula, data = nc, listw = listw)
print(lsrq)
plot(lsrq, sf = nc)
# Version boot
lsrq <- local.sp.runs.test(formula = formula, data = nc, listw = listw,
distr ="bootstrap", nsim = 399)
print(lsrq)
plot(lsrq, sf = nc)
# Case 4: With isolated areas
data(provinces_spain)
listw <- spdep::poly2nb(as(provinces_spain,"Spatial"), queen = FALSE)
provinces_spain$Mal2Fml<- factor(provinces_spain$Mal2Fml > 100)
levels(provinces_spain$Mal2Fml) = c("men","woman")
plot(provinces_spain["Mal2Fml"])
formula <- ~ Mal2Fml
lsrq <- local.sp.runs.test(formula = formula, data = provinces_spain, listw = listw)
print(lsrq)
plot(lsrq, sf = provinces_spain, sig = 0.1)
# Boots Version
lsrq <- local.sp.runs.test(formula = formula, data = provinces_spain, listw = listw,
distr ="bootstrap", nsim = 199)
print(lsrq)
plot(lsrq, sf = provinces_spain, sig = 0.10)
# Case 5: SRQ test based on a distance matrix (inverse distance)
N <- 100
cx <- runif(N)
cy <- runif(N)
coor <- as.data.frame(cbind(cx,cy))
coor <- sf::st_as_sf(coor,coords = c("cx","cy"))
n = dim(coor)[1]
dis <- 1/matrix(as.numeric(sf::st_distance(coor,coor)), ncol = n, nrow = n)
diag(dis) <- 0
dis <- (dis < quantile(dis,.10))*dis
p <- c(1/6,3/6,2/6)
rho <- 0.5
fx <- dgp.spq(p = p, listw = dis, rho = rho)
lsrq <- local.sp.runs.test(fx = fx, listw = dis)
print(lsrq)
plot(lsrq, coor = cbind(cx,cy), sig = 0.05)
lsrq <- local.sp.runs.test(fx = fx, listw = dis, data = )
print(lsrq)
plot(lsrq, sf = coor)
# Version boots
lsrq <- local.sp.runs.test(fx = fx, listw = dis, data = coor,
distr ="bootstrap", nsim = 299)
print(lsrq)
plot(lsrq, sf = coor)
# SRQ test based on inverse distance
data("FastFood.sf")
# sf::sf_use_s2(FALSE)
n = dim(FastFood.sf)[1]
dis <- 1000000/matrix(as.numeric(
sf::st_distance(FastFood.sf, FastFood.sf)),
ncol = n, nrow = n)
diag(dis) <- 0
dis <- (dis < quantile(dis,.01))*dis
formula <- ~ Type
lsrq <- local.sp.runs.test(formula = formula, data = FastFood.sf, listw = dis)
print(lsrq)
# plot(lsrq, sf = FastFood.sf)
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