tropicalPCA.R
Author: Xu Zhang
Date: September 25th 2017
Program: This code produces the 2nd tropical PCA of a small randomly
generated dataset with 20 trees and 8 leaves each in the
theoretical algorithm.
Input: If you want to apply a different size of dataset, then you'll
need to change "DD" and adjust the values of "u" "v" for the
upper bounds in the Propostiion 4.2 in our paper; if you want
a different order of PC, you need to change "pcs". In this
code, pcs is equal to 3 which is the 2nd PC.
Output: "random_sample_20_8.txt" where stores the randomly generated
trees; "random_output_20_8.txt".
tropicalPCA_approx_sim.R
Author: Xu Zhang
Date: September 25th 2017
Program: This code produces the 2nd tropical PCA of simulation dataset in
the heuristic algorithm.
Input: Simulation dataset (If you want to apply a different dataset, then
you'll need to change the path to read the data and adjust
"sum_orig"; if you want a different order of PC, you need to change
"pcs". In this code, pcs is equal to 3 which is the 2nd PC.)
Output: "sim_output_approx_250_8.txt", "proj_sim_250_8_topology.pdf" and
the summary r statistic.
tropicalPCA_approx_apicom.R
Author: Xu Zhang
Date: September 25th 2017
Program: This code produces the 2nd tropical PCA of apicomplexa dataset in
the heuristic algorithm.
Input: Apicomplexa dataset (If you want to apply a different dataset, then
you'll need to change the path to read the data and adjust
"sum_orig"; if you want a different order of PC, you need to change
"pcs". In this code, pcs is equal to 3 which is the 2nd PC.)
Output: "apicom_output_approx.txt", "proj_api_topology.pdf" and the summary
r statistic.