Error using pdist The distance function
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Hello everyone, I have a CSV database, I import this database into mathlab and call them ab_table_Stool_real and Ko_table_Stool_real. However, when I run them in the code below, the following error appears: Error using pdist. The distance function 'distfun_WeightedJaccard' was not found. I would really appreciate it if anyone knows what's going on.
%% Taxonomic diversity, Functional diversity, and Functional redundancy calculation
% filtering
ab_table_real=ab_table_real(:,sum(ab_table_real>0,1)>5);
% Real taxonomic profile
dij_real=pdist(ko_table_real,@distfun_WeightedJaccard);
[SD_real, FD_real, FR_real]=FDFR_Rao_q (ab_table_real, dij_real);
% Null-GCN-1
ko_table_NULL_1=KO_matrix_random(ko_table_real,1);
dij_NULL_1=pdist(ko_table_NULL_1,@distfun_WeightedJaccard);
[SD_NULL_1, FD_NULL_1, FR_NULL_1]=FDFR_Rao_q (ab_table_real, dij_NULL_1);
% Null-GCN-2
ko_table_NULL_2=KO_matrix_random(ko_table_real,2);
dij_NULL_2=pdist(ko_table_NULL_2,@distfun_WeightedJaccard);
[SD_NULL_2, FD_NULL_2, FR_NULL_2]=FDFR_Rao_q (ab_table_real, dij_NULL_2);
% Null-GCN-3
ko_table_NULL_3=KO_matrix_random(ko_table_real,3);
dij_NULL_3=pdist(ko_table_NULL_3,@distfun_WeightedJaccard);
[SD_NULL_3, FD_NULL_3, FR_NULL_3]=FDFR_Rao_q (ab_table_real, dij_NULL_3);
% Null-GCN-4
ko_table_NULL_4=KO_matrix_random(ko_table_real,4);
dij_NULL_4=pdist(ko_table_NULL_4,@distfun_WeightedJaccard);
[SD_NULL_4, FD_NULL_4, FR_NULL_4]=FDFR_Rao_q (ab_table_real, dij_NULL_4);
2 Comments
Star Strider
on 15 Jun 2022
You are apparently using code originally written by someone else, who created the ‘distfun_WeightedJaccard’ function. You will need to look for it in the code you are using, and then put the function somewhere in your MATLAB search path.
Walter Roberson
on 15 Jun 2022
https://github.com/liangtian85/FR/blob/master/distfun_WeightedJaccard.m
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