zenalapp
commented
3 years ago Export:
- [x] get_clusters : function (tr, locs, pureness = 1, bootstrap = NULL)
- [x] get_facility_fsp : function (fasta, locs, form = "matrix")
- [x] get_frac_intra : function (snv_dists = NULL, dists = NULL, locs = NULL, pt = NULL, pt_trans_net = NULL)
- [x] get_patient_transfers : function (pt_trans_net, snv_dists = NULL, dists = NULL, locs = NULL, pt = NULL, thresh = 10, paths = FALSE)
- [x] get_snv_dists : function (dists, locs, pt = NULL, pt_trans_net = NULL)
Don't export:
- [x] %>% : function (lhs, rhs)
- [x] check_allele_freq_input : function (x, subset, allele_n, alleles)
- [x] check_bootstrap : function (bootstrap)
- [x] check_control_labels : function (control_labels)
- [x] check_dists : function (dists)
- [x] check_dists_vs_locs : function (dists, locs)
- [x] check_dna_bin : function (fasta)
- [x] check_facility_fsp_input : function (fasta, locs, form)
- [x] check_fasta_vs_locs : function (fasta, locs)
- [x] check_get_clusters_inputs : function (tr, locs, pureness, bootstrap)
- [x] check_get_frac_intra_input : function (snv_dists, dists, locs, pt, pt_trans_net)
- [x] check_get_largest_subtree_input : function (subtrs, isolate_labels, control_labels, bootstrap, pureness)
- [x] check_get_snv_dists_input : function (dists, locs, pt, pt_trans_net)
- [x] check_locs : function (locs)
- [x] check_long_form_input : function (facil_dist)
- [x] check_paths : function (paths)
- [x] check_pt : function (pt, dists)
- [x] check_pt_trans_net : function (pt_trans_net, locs)
- [x] check_pt_transfer_input : function (pt_trans_net, snv_dists, dists, locs, pt, thresh, paths)
- [x] check_pt_vs_locs : function (pt, locs)
- [x] check_pureness : function (pureness)
- [x] check_reverse_list_str_input : function (ls)
- [x] check_snv_dists : function (snv_dists)
- [x] check_subset_pairs_input : function (snv_dists)
- [x] check_subtrs : function (subtrs, isolate_labels)
- [x] check_subtrs_vs_isolate_labs : function (subtrs, isolate_labels, type)
- [x] check_thresh : function (thresh)
- [x] check_tr_vs_locs : function (tr, locs)
- [x] check_tree : function (tr)
- [x] check_within_pop_var_inputs : function (subset_snp_mat, subset)
- [x] get_allele_freq_btwn : function (x, subset, allele_n, alleles)
- [x] get_allele_freq_within : function (x, allele_n, alleles)
- [x] get_indirect_flow : function (pt_trans_net)
- [x] get_long_form : function (facil_dist)
- [x] get_within_pop_var : function (subset_snp_mat, subset)
- [x] reverse_list_str : function (ls)
- [x] subset_pairs : function (snv_dists)
Decide which functions should be exported and which shouldn't, and reflect that in the code