points.geodata: Plots Spatial Locations and Data Values

Description

This function produces a plot with points indicating the data locations. Arguments can control the points sizes, patterns and colors. These can be set to be proportional to data values, ranks or quantiles. Alternatively, points can be added to the current plot.

Usage

points.geodata(x, coords=x$coords, data=x$data, data.col = 1, borders = NULL,
               pt.divide=c("data.proportional","rank.proportional",
                           "quintiles", "quartiles", "deciles", "equal"),
               lambda = 1, trend = "cte", abs.residuals = FALSE,
               weights.divide = NULL, cex.min, cex.max, cex.var,
               pch.seq, col.seq, add.to.plot = FALSE,
               x.leg, y.leg, dig.leg = 2, 
               round.quantiles = FALSE, graph.pars = FALSE,
               permute = FALSE, ...)

Arguments

a list containing elements coords and data described next. Typically an object of the class "geodata" - a geoR data-set. If not provided the arguments coords and data

coords

an $n \times 2$ matrix containing coordinates of the $n$ data locations in each row. Defaults to geodata$coords.

data

a vector or matrix with data values. If a matrix is provided each column is regarded as one variable or realization. Defaults to geodata$data.

data.col

the number of the data column. Only used if data is a matrix with columns corresponding to different variables or simulations.

borders

If an $n \times 2$ matrix or data-frame with the coordinates of the borders of the regions is provided, the borders are added to the plot.

pt.divide

defines the division of the points in categories. See DETAILS below for the available options. Defaults to pt.divide = "data.proportional".

trend

specifies the mean part of the model. The options are: "cte" (constant mean - default option), "1st" (a first order polynomial on the coordinates), "2nd" (a second order polynomial on the coordinates), or

abs.residuals

logical. If TRUE and teh value passed to the argument trend is different from "cte" the point sizes are proportional to absolute values of the residuals.

lambda

value of the Box-Cox transformation parameter. Two particular cases are $\lambda = 1$ which corresponds to no transformation and $\lambda = 0$ corresponding to the log-transformation.

weights.divide

if a vector of weights with the same length as the data is provided each data is divided by the corresponding element in this vector. Defaults to NULL.

cex.min

minimum value for the graphical parameter cex. This value defines the size of the point corresponding the minimum of the data. Defaults to 0.5.

cex.max

maximum value for the graphical parameter cex. This value defines the size of the point corresponding the maximum of the data. If pt.divide = "equal" it is used to set the value for the graphical parameter c

cex.var

a numeric vector with the values of a variable defining the size of the points.

pch.seq

number(s) defining the graphical parameter pch.

col.seq

number(s) defining the colors in the graphical parameter col.

add.to.plot

logical. If TRUE the points are added to the current plot otherwise a display is open. Defaults to FALSE.

x.leg, y.leg

x and y location of the legend.

dig.leg

integer indicating the precision to be used in the legend values.

round.quantiles

logical. Defines whether or not the values of the quantiles should be rounded. Defaults to FALSE.

graph.pars

logical. If TRUE the graphics parameters used to produce the plots are returned. Defaults to FALSE.

permute

logical indication whether the data values should be randomly re-alocatted to the coordinates. See DETAILS below.

...

further arguments to be passed to the function plot, if add.to.plot = FALSE; or to the function points, if add.to.plot = TRUE.

Value

A plot is created or points are added to the current graphics device. By default no value is returned. However, if graph.pars = TRUE a list with graphical parameters used to produce the plot is returned. According to the input options, the list has some or all of the following components:
quantilesthe values of the quantiles used to divide the data.
cexthe values of the graphics expansion parameter cex.
colthe values of the graphics color parameter col.
pchthe values of the graphics pattern parameter pch.

Details

The points can be devided in categories and have different sizes and/or colours according to the argument pt.divide. The options are: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

For cases where points have different sizes the arguments cex.min and cex.max set the minimum and the maximum point sizes. Additionally, pch.seq can set different patterns for the points and col.seq can be used to define colors. For example, different colors can be used for quartiles, quintiles and deciles while a sequence of gray tones (or a color sequence) can be used for point sizes proportional to the data or their ranks. For more details see the section EXAMPLES.

The argument permute if set to TRUE randomly realocates the data in the coordinates. This may be used to contrast the spatial pattern of original data against another situation where there is no spatial dependence (when setting permute = TRUE). If a trend is provided the residuals (and not the original data) are permuted.

References

Further information on the package geoR can be found at: http://www.est.ufpr.br/geoR.

Examples

Run this code

data(s100)
op <- par(no.readonly = TRUE)
par(mfrow=c(2,2), mar=c(3,3,1,1), mgp = c(2,1,0))
points(s100, xlab="Coord X", ylab="Coord Y")
points(s100, xlab="Coord X", ylab="Coord Y", pt.divide="rank.prop")
points(s100, xlab="Coord X", ylab="Coord Y", cex.max=1.7,
               col=gray(seq(1, 0.1, l=100)), pt.divide="equal")
points(s100, pt.divide="quintile", xlab="Coord X", ylab="Coord Y")
par(op)

data(ca20)
points(ca20, pt.div='quartile', x.leg=4900, y.leg=5850, bor=borders)

par(mfrow=c(1,2), mar=c(3,3,1,1), mgp = c(2,1,0))
points(s100, main="Original data")
points(s100, permute=TRUE, main="Permuting locations")

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