Package index

Running

Functions for starting/stopping the phylotaR pipeline.

setup(): Set-up parameters

run(): Run phylotaR pipeline

restart(): Restart a phylotaR pipeline run

reset(): Reset a phylotaR pipeline run

parameters(): Default parameters

parameters_reset(): Change parameters in a working directory

taxise_run(): Run taxise stage

download_run(): Run download stage

clusters_run(): Run the cluster stage

clusters2_run(): Run the cluster2 stage

Tools

Tools for interacting with the Phylota object

read_phylota(): Generate a Phylota object in R

drop_by_rank(): Reduce clusters to specific rank

drop_clstrs(): Drop cluster records from phylota object

drop_sqs(): Drop sequences in a cluster

get_clstr_slot(): Get slot data for each cluster record

get_sq_slot(): Get slot data for each sequence

get_tx_slot(): Get slot data for each taxon record

get_nsqs(): Count number of sequences

get_ntaxa(): Count number of unique taxa

get_txids(): Get taxonomic IDs by rank

is_txid_in_clstr(): Is txid in cluster?

is_txid_in_sq(): Is txid in sequence?

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

calc_wrdfrq(): Calculate word frequencies

calc_mad(): Calculate MAD score

write_sqs(): Write out sequences

plot_phylota_treemap(): Plot treemap of Phylota object

plot_phylota_pa(): Plot presence/absence matrix

get_stage_times(): Get run times for different stages

Data

Example Phylota objects

aotus: aotus

bromeliads: bromeliads

cycads: cycads

dragonflies: dragonflies

sturgeons: sturgeons

tardigrades: tardigrades

tinamous: tinamous

yeasts: yeasts

Classes

S4 classes

as.character(<ClstrArc>) show(<ClstrArc>) print(<ClstrArc>) str(<ClstrArc>) summary(<ClstrArc>) `[[`(<ClstrArc>,<character>) `[`(<ClstrArc>,<character>,<missing>,<missing>): Cluster record archive

as.character(<ClstrRec>) show(<ClstrRec>) print(<ClstrRec>) str(<ClstrRec>) summary(<ClstrRec>): Cluster record

as.character(<Node>) show(<Node>) print(<Node>) summary(<Node>) `[`(<Node>,<character>,<missing>,<missing>): Node-class

as.character(<Phylota>) show(<Phylota>) print(<Phylota>) str(<Phylota>) summary(<Phylota>) `[[`(<Phylota>,<character>): Phylota object

as.character(<SeqArc>) show(<SeqArc>) print(<SeqArc>) str(<SeqArc>) summary(<SeqArc>) `[[`(<SeqArc>,<character>) `[`(<SeqArc>,<character>,<missing>,<missing>): Sequence record archive

as.character(<SeqRec>) show(<SeqRec>) print(<SeqRec>) str(<SeqRec>) summary(<SeqRec>): Sequence record

as.character(<TaxDict>) show(<TaxDict>) print(<TaxDict>) str(<TaxDict>) summary(<TaxDict>): Taxonomic record dictionary

as.character(<TaxRec>) show(<TaxRec>) print(<TaxRec>) str(<TaxRec>) summary(<TaxRec>): Taxonomic record

`[[`(<TreeMan>,<character>) `[`(<TreeMan>,<character>,<missing>,<missing>) as.character(<TreeMan>) show(<TreeMan>) print(<TreeMan>) str(<TreeMan>) summary(<TreeMan>) cTrees(<TreeMan>): TreeMan-class

cTrees(<TreeMen>) `[[`(<TreeMen>,<ANY>) `[`(<TreeMen>,<character>,<missing>,<missing>) as.character(<TreeMen>) show(<TreeMen>) str(<TreeMen>) print(<TreeMen>) summary(<TreeMen>): TreeMen-class

multiPhylo-class multiPhylo: multiPhylo class

phylo-class phylo: phylo class

Taxise (private)

Internal functions for running the taxise stageuse phylotaR::: to access.

rank_get(): Get rank

descendants_get(): Get descendants

sqs_count(): Count number of sequences for txid

clade_select(): Get all node IDs that will be processed

txnds_count(): Count number of descending taxonomic nodes

txids_get(): Searches for descendant taxonomic IDs

parent_get(): Get taxonomic parent

tax_download(): Download taxonomic records

taxdict_gen(): Generate taxonomic dictionary

taxtree_gen(): Generate taxonomic tree

Download (private)

Internal functions for running the download stageuse phylotaR::: to access.

searchterm_gen(): Construct GenBank Search Term

seq_download(): Download sequences for txids

seqarc_gen(): Generate sequence archive

seqrec_augment(): Augment sequence records list

seqrec_convert(): Convert raw Entrez gb text record to SeqRecs

seqrec_gen(): Generate sequence record

seqrec_get(): seqrec_get

hierarchic_download(): Hierarchically get sequences for a txid

sids_get(): Return random set of sequence IDs

outfmt_get(): Determine 'outformat' format

Cluster (private)

Internal functions for running the cluster stageuse phylotaR::: to access.

blast_clstr(): Cluster BLAST Results

blast_filter(): Filter BLAST results

blast_sqs(): BLAST All vs All

blastdb_gen(): Generate a BLAST database

blastn_run(): Launch blastn

clstr_all(): Hierarchically cluster all sequences of a txid

clstr_direct(): Cluster sequences directly associated with txid

clstr_sqs(): Identify clusters from sequences

clstr_subtree(): Cluster all sequences descending from a txid

clstrarc_gen(): Generate cluster archive container class

clstrarc_join(): Join two cluster archive

clstrrec_gen(): Generate list of clusters

clstrs_calc(): Calculate clusters for all sequences in wd

Cluster2 (private)

Internal functions for running the cluster2 stageuse phylotaR::: to access.

seeds_blast(): BLAST seed sequences

clstr2_calc(): Cluster sets of clusters identified in cluster stage

clstrs_join(): Join clusters for merging

clstrs_merge(): Merge joined clusters

clstrs_renumber(): Renumber cluster IDs

treeman orgin or example datasets

Docs from including treeman

TreeMan-to-phylo: Convert TreeMan to phylo

TreeMen-to-multiPhylo: Convert TreeMen to multiPhylo

addClade(): Add clade to tree

addNdmtrx(): Add node matrix to a tree

addTip(): Add tip to a tree

birds: birds

blncdTree(): Generate a balanced tree

cTrees(): cTrees

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

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

checkNdlst(): Check if ndlst is correct

checkTreeMen(): Check if trees are correct

fastCheckTreeMan(): Check if tree is correct, fast!

getAge(): Get age of tree

getBiprts(): Get the sets of labels for each bipartition in tree

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

getNdSlt(): Get a node slot

getNdSstr(): Get sister id

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

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

getOtgrp(): Get outgroup

getPath(): Get path between nodes

getPrnt(): Get parent

getSpnAge(): Get age range

getSpnsAge(): Get age ranges for multiple nodes

getSubtree(): Get subtree

getUnqNds(): Get unique nodes represented by tips

isUltrmtrc(): Is tree ultrametric?

list-to-TreeMen: Convert list to a TreeMen

loadTreeMan(): Load a TreeMan object in serialization format

mammals: mammals

multiPhylo-to-TreeMen: Convert multiPhylo to TreeMen

phylo-to-TreeMan: Convert phylo to TreeMan

pinTips(): Pin tips to a tree

plants: plants

pstMnp(): Update prinds and tinds

randTree(): Generate a random tree

readTree(): Read a Newick tree

readTrmn(): Read a .trmn tree

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

saveTreeMan(): Save a TreeMan object in serialization format

searchTxnyms(): Get node labels based on online taxonomic database

setAge(): Set the age of a tree

setNdID(): Set the ID of a node

setNdOther(): Set a user defined slot

setNdSpn(): Set the branch length of a specific node

setNdsID(): Set the IDs of multiple nodes

setNdsOther(): Set a user defined slot for multiple nodes

setNdsSpn(): Set the branch lengths of specific nodes

setPD(): Set the phylogenetic diversity

setTxnyms(): Set the txnym slots in a tree

taxaResolve(): Resolve taxonmic names online

twoer(): Generate a tree of two tips

ultrTree(): Make tree ultrametric

unblncdTree(): Generate an unbalanced tree

updateSlts(): Update tree slots after manipulation

writeTree(): Write a Newick tree

writeTrmn(): Write a .trmn tree

Misc (private)

Miscellaneous internal functionsuse phylotaR::: to access.

blast_setup(): Ensures NCBI BLAST tools are installed

download_obj_check(): Check an object returned from rentrez function

safely_connect(): Safely run rentrez function

search_and_cache(): Run rentrez function and cache results

batcher(): Download in batches

info(): Write info message to log

error(): Write error message to log

warn(): Write warning message to log

blastcache_load(): Load BLAST results from cache

blastcache_save(): Save BLAST results to cache

sids_check(): Check if sids exist

sids_load(): Load sids from cache

sids_save(): Save sids to cache

cache_rm(): Delete a cache

cache_setup(): Set-up a cache

sqs_save(): Save sequences to cache

ncbicache_load(): Retrieve cached NCBI query

ncbicache_save(): Save NCBI query result to cache

stages_run(): Sequentially run each stage

stage_args_check(): Check stage arguments

mk_txid_in_sq_mtrx(): Return matrix of txid in sequence

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

summary_phylota(): Summarise clusters in Phylota Table

parameters_load(): Load parameters from cache

progress_init(): Initialise progress list in cache

progress_read(): Read the progress from cache

progress_reset(): Reset progress

progress_save(): Save current progress

cmdln(): Run a command via terminal/command prompt

update_phylota(): Update slots

parameters_setup(): Set Up Parameters

clstrs_save(): Save clusters to cache

gb_extract(): Extract elements from a raw GenBank record

rawseqrec_breakdown(): Breakdown a sequence record into its features