RMSD.idturtle: Compare by pairs all the measurements in the database

In IDTurtle: Identify Turtles by their Plastral Biometries

Description

Create a dataframe with the RMSD of all the possible pairs of measurements. This is useful to plot a tree grouping the closests measurements. This tool allow an easy visualization of measurements far away to other from the same turtle, which can be errors in the identification or in the measurements.

Usage

RMSD.idturtle(data, ID = "ID", date = "date", PL = "PL", GuL = "GuL", HumL = "HumL",
PecL = "PecL", AbdL = "AbdL", FemL = "FemL", AnL = "AnL")

Arguments

data	Dataframe with the database of all the measurements of all the specimens
ID	Name of the identification code of the turtle column in both data.comp and data.ref
date	Name of the column with the date in both data.comp and data.ref
PL	Name of the plastral length column in both data.comp and data.ref
GuL	Name of the intergular length column in both data.comp and data.ref
HumL	Name of the interhumeral length column in both data.comp and data.ref
PecL	Name of the interpectoral length column in both data.comp and data.ref
AbdL	Name of the interabdominal length column in both data.comp and data.ref
FemL	Name of the interfemoral length column in both data.comp and data.ref
AnL	Name of the interanal length column in both data.comp and data.ref

Value

It returns a data frame with all the measurements sets of each turtle in each capture event in both row and columns as a 2D matrix. A clustering dendrogram can be plotted with the function cluster.RMSD

Note

This is a time comsuming analysis which compare two by two all the possible pairs of measures of turtles, identifying each one with the ID followed by the date.

Author(s)

Aitor Valdeon

Examples

#Charge and prepare example data
data(data.comp,data.ref)
comp<-data.comp[1:20,]
ref<-data.comp[!(1:nrow(data.comp)),]
cont<-0
repeat{
  cont<-cont+1
  r<-data.ref[data.ref$ID==comp[cont,c("ID")],]
  ref<-rbind(ref,r)
  if(cont==20){
    break
  }
}
data.RMSD<-rbind(comp,ref)
#Delete non-interesting objects for this action
rm(cont,r,data.comp,data.ref,comp,ref)
#Execute RMSD.idturtle. Column date in data.RMSD is named in spanish (Fecha)
RMSD<-RMSD.idturtle(data.RMSD,date="Fecha")

IDTurtle documentation built on May 30, 2017, 7:39 a.m.