Dynamic Estimator of Microbial Communities
Generate a variety of stats on PTR estimates for a given dataset
A function for iteration of pipeline until convergence
A convenient function for KS test of uniform distribution
A convenient function for ordinary linear regression on two vectors
Run mixed linear model with random effect using lme4
A function representing the pipeline of four steps including GC bias c...
A function for reshape to facilitate PCA, removing all contigs with mi...
A function to remove outlier contigs using KS test
A function to test whether the result is reasonable
Verify that the input dataframe/matrix is valid
Compares contig subset x against contig subset y
Compares sample subset x against sample subset y
A function for data frame integration
A function to return the first dimension of PCA on an input matrix
Determine the majority orientation of the input PTR estimates correlat...
A function for data frame transfer
Estimate PTRs using all input data as well as using subsets of contigs...
Tries up to max_attempts times to compare each permutation of removing...
Estimates PTRs based on the whole input dataset
Get PTR estimates for output of the core pipeline on a subset of data
A function for sample filtration Input requirements: 1. have values in...
Multi-sample algorithm based on contigs and coverage values, to infer the relative distances of contigs from the replication origin and to accurately compare bacterial growth rates between samples. Yuan Gao and Hongzhe Li (2018) <doi:10.1038/s41592-018-0182-0>.