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