# Dynamic Estimator of Microbial Communities

## Documentation for package ‘demic’ version 2.0.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

compare_contig_subsets | Compares contig subset x against contig subset y
compare_sample_subsets | Compares sample subset x against sample subset y
consist_transfer | A function for data frame integration
ContigCluster1 | Contig Cluster 1
ContigCluster2 | Contig Cluster 2
contig_pca | A function to return the first dimension of PCA on an input matrix
cor_diff | Determine the majority orientation of the input PTR estimates correlations
df_transfer | A function for data frame transfer
est_ptr | Estimate PTRs using all input data as well as using subsets of contigs and samples
est_ptrs_subset | Get PTR estimates for output of the core pipeline on a subset of data
est_ptr_on | Tries up to max_attempts times to compare each permutation of removing random subsets of contigs/samples from X, and returns the PTR estimate if a valid one comes back from the comparisons
est_ptr_on_all | Estimates PTRs based on the whole input dataset
filter_sample | A function for sample filtration Input requirements: 1. have values in more than half of the contigs 2. average log2(cov) > 0 in all these contigs
get_eptr_stats | Generate a variety of stats on PTR estimates for a given dataset
iterate_pipelines | A function for iteration of pipeline until convergence
ks | A convenient function for KS test of uniform distribution
lme4_model | Run mixed linear model with random effect using lme4
lm_column | A convenient function for ordinary linear regression on two vectors
max_bin_001 | MaxBin2 Cluster 001
max_bin_002 | MaxBin2 Cluster 002
max_bin_003 | MaxBin2 Cluster 003
pipeline | A function representing the pipeline of four steps including GC bias correction, sample filtration, PCA and contig filtration
reshape_filtered | A function for reshape to facilitate PCA, removing all contigs with missing values for designated samples
select_by_ks_test | A function to remove outlier contigs using KS test
test_reasonable | A function to test whether the result is reasonable
verify_input | Verify that the input dataframe/matrix is valid