Man pages for ropensci/phylotaR
Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
| addClade | Add clade to tree |
| addNdmtrx | Add node matrix to a tree |
| addTip | Add tip to a tree |
| aotus | aotus |
| batcher | Download in batches |
| birds | birds |
| blastcache_load | Load BLAST results from cache |
| blastcache_save | Save BLAST results to cache |
| blast_clstr | Cluster BLAST Results |
| blastdb_gen | Generate a BLAST database |
| blast_filter | Filter BLAST results |
| blastn_run | Launch blastn |
| blast_setup | Ensures NCBI BLAST tools are installed |
| blast_sqs | BLAST All vs All |
| blncdTree | Generate a balanced tree |
| bromeliads | bromeliads |
| cache_rm | Delete a cache |
| cache_setup | Set-up a cache |
| calcDstBLD | Calculate the BLD between two trees |
| calcDstMtrx | Calculate the distance matrix |
| calcDstRF | Calculate the Robinson-Foulds distance between two trees |
| calcDstTrp | Calculate the triplet distance between two trees |
| calcFrPrp | Calculate evolutionary distinctness |
| calc_mad | Calculate MAD score |
| calcNdBlnc | Calculate the balance of a node |
| calcNdsBlnc | Calculate the balances of all nodes |
| calcOvrlp | Calculate phylogenetic overlap |
| calcPhyDv | Calculate phylogenetic diversity |
| calcPrtFrPrp | Calculate evolutionary distinctness for part of tree |
| calc_wrdfrq | Calculate word frequencies |
| checkNdlst | Check if ndlst is correct |
| checkTreeMen | Check if trees are correct |
| clade_select | Get all node IDs that will be processed |
| clstr2_calc | Cluster sets of clusters identified in cluster stage |
| clstr_all | Hierarchically cluster all sequences of a txid |
| ClstrArc-class | Cluster record archive |
| clstrarc_gen | Generate cluster archive container class |
| clstrarc_join | Join two cluster archive |
| clstr_direct | Cluster sequences directly associated with txid |
| ClstrRec-class | Cluster record |
| clstrrec_gen | Generate list of clusters |
| clstrs_calc | Calculate clusters for all sequences in wd |
| clstrs_join | Join clusters for merging |
| clstrs_merge | Merge joined clusters |
| clstr_sqs | Identify clusters from sequences |
| clstrs_renumber | Renumber cluster IDs |
| clstrs_save | Save clusters to cache |
| clstr_subtree | Cluster all sequences descending from a txid |
| clusters2_run | Run the cluster2 stage |
| clusters_run | Run the cluster stage |
| cmdln | Run a command via terminal/command prompt |
| cTrees | cTrees |
| cycads | cycads |
| descendants_get | Get descendants |
| download_obj_check | Check an object returned from rentrez function |
| download_run | Run download stage |
| dragonflies | dragonflies |
| drop_by_rank | Reduce clusters to specific rank |
| drop_clstrs | Drop cluster records from phylota object |
| drop_sqs | Drop sequences in a cluster |
| error | Write error message to log |
| fastCheckTreeMan | Check if tree is correct, fast! |
| gb_extract | Extract elements from a raw GenBank record |
| getAge | Get age of tree |
| getBiprts | Get the sets of labels for each bipartition in tree |
| get_clstr_slot | Get slot data for each cluster record |
| getCnnctdNds | Get all nodes connected by given tips |
| getDcsd | Get extinct tips from a tree |
| getLvng | Get extant tips from a tree |
| getNdAge | Get age |
| getNdKids | Get children IDs |
| getNdLng | Get lineage |
| getNdPD | Get phylogenetic diversity of node |
| getNdPrdst | Get pre-distance |
| getNdPrids | Get pre-nodes to root |
| getNdPtids | Get post-nodes to tips |
| getNdsAge | Get ages for multiple nodes |
| getNdsFrmTxnyms | Get IDs for nodes represented txnyms |
| getNdsKids | Get children IDs for multiple nodes |
| getNdsLng | Get lineage for multiple nodes |
| getNdSlt | Get a node slot |
| getNdsPD | Get phylogenetic diversities of nodes |
| getNdsPrdst | Get pre-distances |
| getNdsPrids | Get pre-nodes for multiple nodes |
| getNdsPtids | Get post-nodes to tips for multiple nodes |
| getNdsSlt | Get a node slot for multiple nodes |
| getNdsSstr | Get sister id |
| getNdSstr | Get sister id |
| get_nsqs | Count number of sequences |
| get_ntaxa | Count number of unique taxa |
| getOtgrp | Get outgroup |
| getPath | Get path between nodes |
| getPrnt | Get parent |
| getSpnAge | Get age range |
| getSpnsAge | Get age ranges for multiple nodes |
| get_sq_slot | Get slot data for each sequence |
| get_stage_times | Get run times for different stages |
| getSubtree | Get subtree |
| get_txids | Get taxonomic IDs by rank |
| get_tx_slot | Get slot data for each taxon record |
| getUnqNds | Get unique nodes represented by tips |
| hierarchic_download | Hierarchically get sequences for a txid |
| info | Write info message to log |
| is_txid_in_clstr | Is txid in cluster? |
| is_txid_in_sq | Is txid in sequence? |
| isUltrmtrc | Is tree ultrametric? |
| list_clstrrec_slots | List all ClstrRec slots |
| list_ncbi_ranks | List all NCBI Ranks |
| list_seqrec_slots | List all SeqRec slots |
| list_taxrec_slots | List all TaxRec slots |
| list-to-TreeMen | Convert list to a TreeMen |
| loadTreeMan | Load a TreeMan object in serialization format |
| mammals | mammals |
| mk_txid_in_sq_mtrx | Return matrix of txid in sequence |
| multiPhylo-class | multiPhylo class |
| multiPhylo-to-TreeMen | Convert multiPhylo to TreeMen |
| ncbicache_load | Retrieve cached NCBI query |
| ncbicache_save | Save NCBI query result to cache |
| Node-class | Node-class |
| obj_check | Check if an object exists |
| obj_load | Load a named object from the cache |
| obj_save | Save a named object in the cache |
| outfmt_get | Determine 'outformat' format |
| parameters | Default parameters |
| parameters_load | Load parameters from cache |
| parameters_reset | Change parameters in a working directory |
| parameters_setup | Set Up Parameters |
| parent_get | Get taxonomic parent |
| phylo-class | phylo class |
| Phylota-class | Phylota object |
| phylo-to-TreeMan | Convert phylo to TreeMan |
| pinTips | Pin tips to a tree |
| plants | plants |
| plot_phylota_pa | Plot presence/absence matrix |
| plot_phylota_treemap | Plot treemap of Phylota object |
| progress_init | Initialise progress list in cache |
| progress_read | Read the progress from cache |
| progress_reset | Reset progress |
| progress_save | Save current progress |
| pstMnp | Update prinds and tinds |
| randTree | Generate a random tree |
| rank_get | Get rank |
| rawseqrec_breakdown | Breakdown a sequence record into its features |
| read_phylota | Generate a Phylota object in R |
| readTree | Read a Newick tree |
| readTrmn | Read a .trmn tree |
| reset | Reset a phylotaR pipeline run |
| restart | Restart a phylotaR pipeline run |
| rmClade | Remove a clade from a tree |
| rmNdmtrx | Remove node matrix |
| rmNodes | Remove nodes from a tree |
| rmOtherSlt | Remove a user-defined slot |
| rmTips | Remove tips from a tree |
| run | Run phylotaR pipeline |
| safely_connect | Safely run rentrez function |
| saveTreeMan | Save a TreeMan object in serialization format |
| search_and_cache | Run rentrez function and cache results |
| searchterm_gen | Construct GenBank Search Term |
| searchTxnyms | Get node labels based on online taxonomic database |
| seeds_blast | BLAST seed sequences |
| SeqArc-class | Sequence record archive |
| seqarc_gen | Generate sequence archive |
| seq_download | Download sequences for txids |
| seqrec_augment | Augment sequence records list |
| SeqRec-class | Sequence record |
| seqrec_convert | Convert raw Entrez gb text record to SeqRecs |
| seqrec_gen | Generate sequence record |
| seqrec_get | seqrec_get |
| setAge | Set the age of a tree |
| setNdID | Set the ID of a node |
| setNdOther | Set a user defined slot |
| setNdsID | Set the IDs of multiple nodes |
| setNdsOther | Set a user defined slot for multiple nodes |
| setNdSpn | Set the branch length of a specific node |
| setNdsSpn | Set the branch lengths of specific nodes |
| setPD | Set the phylogenetic diversity |
| setTxnyms | Set the txnym slots in a tree |
| setup | Set-up parameters |
| sids_check | Check if sids exist |
| sids_get | Return random set of sequence IDs |
| sids_load | Load sids from cache |
| sids_save | Save sids to cache |
| sqs_count | Count number of sequences for txid |
| sqs_save | Save sequences to cache |
| stage_args_check | Check stage arguments |
| stages_run | Sequentially run each stage |
| sturgeons | sturgeons |
| summary_phylota | Summarise clusters in Phylota Table |
| tardigrades | tardigrades |
| taxaResolve | Resolve taxonmic names online |
| TaxDict-class | Taxonomic record dictionary |
| taxdict_gen | Generate taxonomic dictionary |
| tax_download | Download taxonomic records |
| taxise_run | Run taxise stage |
| TaxRec-class | Taxonomic record |
| taxtree_gen | Generate taxonomic tree |
| tinamous | tinamous |
| TreeMan-class | TreeMan-class |
| TreeMan-to-phylo | Convert TreeMan to phylo |
| TreeMen-class | TreeMen-class |
| TreeMen-to-multiPhylo | Convert TreeMen to multiPhylo |
| twoer | Generate a tree of two tips |
| txids_get | Searches for descendant taxonomic IDs |
| txnds_count | Count number of descending taxonomic nodes |
| ultrTree | Make tree ultrametric |
| unblncdTree | Generate an unbalanced tree |
| update_phylota | Update slots |
| updateSlts | Update tree slots after manipulation |
| warn | Write warning message to log |
| write_sqs | Write out sequences |
| writeTree | Write a Newick tree |
| writeTrmn | Write a .trmn tree |
| yeasts | yeasts |
