biodecrypt.cross: Perform a cross validation analysis to test the attribution...

In leondap/recluster: Ordination Methods for the Analysis of Beta-Diversity Indices

Perform a cross validation analysis to test the attribution of biodecrypt on attributed records

Description

The function biodecrypt.cross wraps the biodecrypt function to carry out cross-validation of known cases thus verifying the robustness of the attribution of unknown cases. This function requires the same input of biodecrypt (coordinates and vector with attribution together with values of distance ratio, buffer and alpha). Moreover this function requires a "runs" value defining the number of different runs, thus the fraction of test records included in each run. In each run, randomly selected group of test records (actually identified to a given species) are regarded as unidentified (0 value) and the biodecrypt function is carried out to attribute them. The analysis is repeated as often as defined in runs (a runs value of 10 will perform a ten-fold cross-validation based on the initial selection of ten randomly distributed subsets).

Usage

biodecrypt.cross(mat,id,alpha=NULL,ratio=2.5,buffer=90,fraction=0.95, partCount = 10, 
checkdist=T, clipToCoast="terrestrial", proj = "+proj=longlat +datum=WGS84",minimum=7,
map=NULL,xlim=NULL,ylim=NULL,main=NULL,runs=10,test=T)

Arguments

mat	A matrix for longitude and latitude (in decimal degrees) for all records.
id	A vector indicating species membership of each record (in the same order of mat). Identified records are indicated with 1,2..n, unidentified records with 0.
alpha	A vector indicating an initial alpha value for each species. If NULL, the default value of 8 for all species is used.
ratio	The minimum ratio between the distance from the second distant hull compared to the closest hull to allow attribution. Default 2.5 times.
buffer	A distance buffer from hulls(in km).
fraction	The minimum fraction of occurrences that must be included in polygon.
partCount	The maximum number of disjunct polygons that are allowed..
clipToCoast	Either "no" (no clipping), "terrestrial" (only terrestrial part of range is kept) or "aquatic" (only non-terrestrial part is clipped).
checkdist	Logical, if TRUE cases attributed to a given species based on relative distance from hulls but closer to an identified record of another species are not attributed.
proj	the projection information for mat. In this version, the default is the only supported option.
minimum	The minimum number of specimens required to build alpha hulls. If the number of identified specimens is lower, convex hulls are calculated to improve procedure stability.
map	A map to be plotted during the procedure to show the separation progress.
xlim	Longitude boudaries for the map.
ylim	latitude boudaries for the map.
main	The name to be plotted on the graph
runs	The number of runs among which the cases are randomly assigned as non-attributed records
test	A logical, if TRUE, a biodecrypt analysis is also carried out to compute NUR.

Details

The procedure attributes the subsets of identified records to the test group (unknown cases) as evenly as possible among runs both in terms of total number of test records and records belonging to the same original species. If the number of runs equates the number of records, then each identified record is individually attributed in a jackknife procedure. Subsequently, the attribution vector obtained is provided and compared with the original membership and two values are provided: the percentages of identified cases attributed to a wrong species (Mis-Identified Records, MIR) and the percentage of known cases not attributed to any species (Non-attributed Identified Records, NIR). The function also has an option to calculate the percentage of Non-attributed Unidentified Records (NUR) representing the fraction of unknown records that could not be attributed to a species after a typical biodecrypt analysis using the parameters provided by the user and the complete set of records.

Value

type	"cross" an argument to be passed to biodecrypt.plot.
NUR	The percentage of Non-attributed Unidentified Records.
areas	The hull areas for all the species (in km squares).
intersections	The areas of intersections among hulls for each pair of species.
sympatry	The fraction of the overlap area compared to the total area of the two hulls.
table	The result table of the test (if test=TRUE) with Longitude and Latitude for each occurrence datum, its id after the biodecrypt procedure (id2) and its initial id (id).
cross	The result table with the original attribution (original), the attribution obtained after cross validation (predicted) and the classification as MIR or NIR. Longitude and Latitude are also provided.
MIR	The percentage of Mis-Identified Records.
NIR	The percentage of Non-Identified Records.

Author(s)

Leonardo Dapporto

References

Platania L. et al. Assigning occurrence data to cryptic taxa improves climatic niche assessments: biodecrypt, a new tool tested on European butterflies. Glocal Ecology and Biogeography (2020).

Examples

## Not Run
## Create an example for a dataset

#mat<-rbind(cbind(rnorm(n = 20, mean = 1, sd = 4),rnorm(n = 20, mean = 40, sd = 3)),
#cbind(rnorm(n = 20, mean = 7, sd = 5),rnorm(n = 20, mean = 45, sd = 2))

#id<-c(rep(1,20),rep(2,20))
#id[sample(c(1:40))[1:10]]<-0

#cross<-biodecrypt.cross(mat,id)
#plot(mat,type="n")
#biodecrypt.plot(cross)

leondap/recluster documentation built on Nov. 11, 2024, 7:11 a.m.