| compare.dist | R Documentation |
This function implements the Lefebure's method to quantify the overlap between two distributions and to determine the best threshold value to discriminate them.
compare.dist(distr1=NULL,distr2=NULL,N=50,
normalize=TRUE,main=NA,col1="gray",col2="black",
col.border1="gray",col.border2="black",
col.line1="gray",col.line2="black",
Ylab=c("Abundance","Abundance","Success"),
Xlab=c("data1","data2","Threshold"))
distr1 |
a matrix containing the pairwise genetic distances between individual sequences |
distr2 |
a vector containing the minimum and maximum value in the x-axis |
N |
a numeric, the number of categories for the x-axis. |
normalize |
a logic, "TRUE" to display percentage and "FALSE" for number of occurrences in the Y axis. |
main |
a vector with two elements containing the main titles of both plots. |
col1 |
a string, the color to fill the histogram for distribution 1 |
col2 |
a string, the color to fill the histogram for distribution 2 |
col.border1 |
a string, the color for the border around the histogram for distribution 1 |
col.border2 |
a string, the color for the border around the histogram for distribution 2 |
col.line1 |
a string, the color for the line representing distribution 1 |
col.line2 |
a string, the color for the line representing distribution 2 |
Ylab |
a three strings vector containing the labels of Y axes for the three plots to be represented. |
Xlab |
a three strings vector containing the labels of X axes for the three plots to be represented |
The estimated threshold and its success of identification.
A.J. Muñoz-Pajares
Lefébure T, Douady CJ, Gouy M, Gibert J (2006). Relationship between morphological taxonomy and molecular divergence within Crustacea: Proposal of a molecular threshold to help species delimitation. Mol Phylogenet Evol 40: 435–447.
# ## Weak overlap # intra<-rnorm(mean=0.08,sd=0.04,n=100) # inter<-rnorm(mean=0.38,sd=0.10,n=1000) # intra[intra<0]<-0 # inter[inter<0]<-0 # compare.dist(distr1=intra,distr2=inter,N=50) # # # Strong overlap # distr1<-rnorm(5000,mean=0.25,sd=0.070) # distr2<-rnorm(5000,mean=0.31,sd=0.075) # N<-50 # compare.dist(distr1,distr2,N) #