R: Converts an Object to the Class "geodata"

as.geodata {geoR} | R Documentation

## Converts an Object to the Class "geodata"

### Description

The default method converts a matrix or a data-frame to an object of the `class` `"geodata"`.
Objects of the class `"geodata"` are lists with two obligatory components: `coords` and `data`. Optional components are allowed and a typical example is a vector or matrix with covariate(s) values.

### Usage

    as.geodata(obj, ...)

    ## Default S3 method:
    as.geodata(obj, coords.col = 1:2, data.col = 3, data.names = NULL,
                       covar.col = NULL, covar.names = "obj.names",
                       units.m.col = NULL, realisations = NULL,
                       na.action = c("ifany", "ifdata", "ifcovar", "none"),
                       rep.data.action, rep.covar.action, rep.units.action,
                       ...)

    ## S3 method for class 'geodata'
    as.data.frame(x, ..., borders = TRUE)

    ## S3 method for class 'geodata.frame'
    as.geodata(obj, ...)

    ## S3 method for class 'SpatialPointsDataFrame'
    as.geodata(obj, data.col = 1, ...)

    is.geodata(x)

### Arguments

`obj` | a matrix or data-frame where each line corresponds to one spatial location. It should contain values of 2D coordinates, data and, optionally, covariate(s) value(s) at the locations. A method for `SpatialPointsDataFrame` is also provided. It can also take an output of the function `grf`, see DETAILS below.
`coords.col` | a vector with the column numbers corresponding to the spatial coordinates.
`data.col` | a scalar or vector with column number(s) corresponding to the data.
`data.names` | optional. A string or vector of strings with names for the data columns. Only valid if there is more than one column of data. By default, takes the names from the original object.
`covar.col` | optional. A scalar or numeric vector with the column number(s) corresponding to the covariate(s). Alternativelly can be a character vector with the names of the covariates.
`covar.names` | optional. A string or vector of strings with the name(s) of the covariates. By default take the names from the original object.
`units.m.col` | optional. A scalar with the column number corresponding to the offset variable. Alternativelly can be a character vector with the name of the offset. This option is particularly relevant when using the package geoRglm. All values must be greater then zero.
`realisations` | optional. A vector indicating the realisation number or a number indicating a column in `obj` with the realisation indicator variable. See `DETAILS` below.
`na.action` | string defining action to be taken in the presence of `NA`'s. The default option `"ifany"` excludes all points for which there are `NA`'s in the data or covariates. The option `"ifdata"` excludes points for which there are `NA`'s in the data. The default option `"ifcovar"` excludes all points for which there are `NA`'s in the covariates. The option `"none"` do not exclude points.
`rep.data.action` | a string or a function. Defines action to be taken when there is more than one data at the same location. The default option `"none"` keeps the repeated locations, if any. The option `"first"` retains only the first data recorded at each location. Alternativelly a function can be passed and it will be used. For instance if `mean` is provided, the function will compute and return the average of the data at coincident locations. The non-default options will eliminate the repeated locations.
`rep.covar.action` | idem to `rep.data.locations`, to be applied to the covariates, if any. Defaults to the same option set for `rep.data.locations`.
`x` | an object which is tested for the class `geodata`.
`rep.units.action` | a string or a function. Defines action to be taken on the element `units.m`, if present when there is more than one data at the same location. The default option is the same value set for `rep.data.action`.
`borders` | logical. If TRUE the element borders in the `geodata` object is set as an attribute of the data-frame.
`...` | values to be passed for the methods.

### Details

Objects of the class `"geodata"` contain data for geostatistical analysis using the package geoR. Storing data in this format facilitates the usage of the functions in geoR. However, conversion of objects to this class is not obligatory to carry out the analysis.

`NA`'s are not allowed in the coordinates. By default the respective rows will not be included in the output.

Realisations
Tipically geostatistical data correspond to a unique realisation of the spatial process. However, sometimes different "realisations" are possible. For instance, if data are collected in the same area at different points in time and independence between time points is assumed, each time can be considered a different "replicate" or "realisation" of the same process. The argument `realisations` takes a vector indication the replication number and can be passed to other geoR functions as, for instance, `likfit`.

The data format is similar to the usual `geodata` format in geoR. Suppose there are realisations (times) 1, ..., J and for each realisations n_1, ..., n_j observations are available. The coordinates for different realisations should be combined in a single nx2 object, where n=n_1 + ... + n_J. Similarly for the data vector and covariates (if any).

grf objects
If an object of the class `grf` is provided the functions just extracts the elements `coords` and `data` of this object.

### Value

An object of the `class` `"geodata"` which is a list with two obligatory components (coords and data) and other optional components:

`coords` | an n \times 2 matrix where n is the number of spatial locations.
`data` | a vector of length n, for the univariate case or, an n \times v matrix or data-frame for the multivariate case, where v is the number of variables.
`covariates` | a vector of length n or an n \times p matrix with covariate(s) values, where p is the number of covariates. Only returned if covariates are provided.
`realisations` | a vector on size n with the replication number. Only returned if argument realisations is provided.

### Author(s)

Paulo Justiniano Ribeiro Jr. paulojus@leg.ufpr.br,
Peter J. Diggle p.diggle@lancaster.ac.uk.

### References

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

### See Also

`read.geodata` for reading data from an ASCII file and `list` for general information on lists.

### Examples

    ## Not run:
    ## converting the data-set "topo" from the package MASS (VR's bundle)
    ## to the geodata format:
    if(require(MASS)){
    topo
    topogeo <- as.geodata(topo)
    names(topogeo)
    topogeo
    }

    ## End(Not run)

[Package geoR version 1.7-5.2 Index]