RaoAUC | R Documentation |
RaoAUC computes the accumulation function (integral or area under the curve) of the parametric version of Rao's index of quadratic entropy (Q) on different classes of numeric matrices using a moving window algorithm.
RaoAUC(alphas=1:5, x, dist_m="euclidean", window=9, method="classic", rasterAUC=TRUE, lambda=0, na.tolerance=1.0, rescale=FALSE, diag=TRUE, simplify=2, np=1, cluster.type="SOCK", debugging=FALSE)
alphas |
a continuous vector of alphas in the form start:end over which integrated the parametric Rao's index. Default value is 1:5. |
x |
input data may be a matrix, a Spatial Grid Data Frame, a RasterLayer or a list of these objects. In the latter case, if |
dist_m |
define the type of distance to be calculated between numerical categories. |
window |
the side of the square moving window, it must be a odd numeric value greater than 1 to ensure that the target pixel is in the centre of the moving window. Default value is 3. If |
method |
Currently, there are two ways to calculate the parametric version of Rao's index. If |
rasterAUC |
Boolean, if TRUE the output will be a RasterLayer object with x as a raster template. |
lambda |
the value of the lambda of Minkowski's distance. Considered only if |
na.tolerance |
Numeric value (0.0-1.0) which indicates the proportion of NA values that will be tolerated to calculate parametric Rao's index in each moving window over x. If the relative proportion of NA's in a moving window is bigger than na.tolerance, then the value of the window will be set as NA, otherwise Rao's index will be calculated considering the non-NA values. Default values is 1.0 (i.e., no tolerance for NA's). Default value is 1.0. |
rescale |
Boolean. Considered only if |
diag |
Boolean. If TRUE then the diagonal of the distance matrix is filled with 0's, otherwise with NA's. If |
simplify |
Number of decimal places to be retained to calculate distances in Rao's index. Only if x is floats. |
np |
the number of processes (cores) which will be spawned. Default value is 2. |
cluster.type |
the type of cluster which will be created. The options are "MPI" (which calls "makeMPIcluster"), "FORK" and "SOCK" (which call "makeCluster"). Default type is "SOCK". |
debugging |
a boolean variable set to FALSE by default. If TRUE, additional messages will be printed. For debugging only. |
The accumulation function for the parametric Rao's Index (Q) is calculated integrating numerically over a range of alphas. *RaoAUC* is therefore equal to (\int_{a}^{b} {1\over{N^4}}\cdot{d_{i,j}^{α}})^{1\over{α}} dx. Where N is the number of pixels in a moving window, and alpha is a weight assigned to distances.
A matrix of dimension dim(x)
. If rasterAUC=TRUE
, then the output is a RasterLayer with x as template.
Matteo Marcantonio marcantoniomatteo@gmail.com
[1] Rocchini, D., M. Marcantonio, and C. Ricotta (2017). Measuring Rao’s Q diversity index from remote sensing: An open source solution. Ecological Indicators. 72: 234–238.
paRao
#Minimal example; RaoAUC with alphas ranging from 1 to 10 a <- matrix(c(10,10,10,20,20,20,20,30,30), ncol=3, nrow=3) out <- RaoAUC(alphas=1:10, x=a, window=3, dist_m="euclidean", na.tolerance=1, rasterAUC=TRUE)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.