IDTurtle (version 1.2)

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

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

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")