_pkgdown.yml

navbar:
  structure:
    left:
    - home
    - intro
    - reference
    - news
    right: github
  components:
    home:
      icon: fa-home fa-lg
      href: index.html
    reference:
      text: Reference
      href: reference/index.html
    intro:
      text: Get started
      href: articles/phylotaR.html
    news:
      text: Changelog
      href: news/index.html
    github:
      icon: fa-github fa-lg
      href: https://github.com/ropensci/phylotaR
reference:
- title: Running
  desc:  Functions for starting/stopping the phylotaR pipeline.
  contents:
    - setup
    - run
    - restart
    - reset
    - parameters
    - parameters_reset
    - taxise_run
    - download_run
    - clusters_run
    - clusters2_run
- title: Tools
  desc: Tools for interacting with the Phylota object
  contents:
    - read_phylota
    - drop_by_rank
    - drop_clstrs
    - drop_sqs
    - get_clstr_slot
    - get_sq_slot
    - get_tx_slot
    - get_nsqs
    - get_ntaxa
    - get_txids
    - is_txid_in_clstr
    - is_txid_in_sq
    - list_clstrrec_slots
    - list_ncbi_ranks
    - list_seqrec_slots
    - list_taxrec_slots
    - calc_wrdfrq
    - calc_mad
    - write_sqs
    - plot_phylota_treemap
    - plot_phylota_pa
    - get_stage_times
- title: Data
  desc: Example Phylota objects
  contents:
    - aotus
    - bromeliads
    - cycads
    - dragonflies
    - sturgeons
    - tardigrades
    - tinamous
    - yeasts
- title: Classes
  desc: S4 classes
  contents:
    - ends_with("-class")
- title: Taxise (private)
  desc: Internal functions for running the taxise stageuse `phylotaR:::` to access.
  contents:
    - rank_get
    - descendants_get
    - sqs_count
    - clade_select
    - txnds_count
    - txids_get
    - parent_get
    - tax_download
    - taxdict_gen
    - taxtree_gen
- title: Download (private)
  desc: Internal functions for running the download stageuse `phylotaR:::` to access.
  contents:
    - searchterm_gen
    - seq_download
    - seqarc_gen
    - seqrec_augment
    - seqrec_convert
    - seqrec_gen
    - seqrec_get
    - hierarchic_download
    - sids_get
    - outfmt_get
- title: Cluster (private)
  desc: Internal functions for running the cluster stageuse `phylotaR:::` to access.
  contents:
    - blast_clstr
    - blast_filter
    - blast_sqs
    - blastdb_gen
    - blastn_run
    - clstr_all 
    - clstr_direct
    - clstr_sqs
    - clstr_subtree
    - clstrarc_gen
    - clstrarc_join
    - clstrrec_gen
    - clstrs_calc
- title: Cluster2 (private)
  desc: Internal functions for running the cluster2 stageuse `phylotaR:::` to access.
  contents:
    - seeds_blast
    - clstr2_calc
    - clstrs_join
    - clstrs_merge
    - clstrs_renumber
- title: treeman orgin or example datasets
  desc: Docs from including treeman
  contents:
    - TreeMan-to-phylo
    - TreeMen-to-multiPhylo
    - addClade
    - addNdmtrx
    - addTip
    - birds
    - blncdTree
    - cTrees
    - calcDstBLD
    - calcDstMtrx
    - calcDstRF
    - calcDstTrp
    - calcFrPrp
    - calcNdBlnc
    - calcNdsBlnc
    - calcOvrlp
    - calcPhyDv
    - calcPrtFrPrp
    - checkNdlst
    - checkTreeMen
    - fastCheckTreeMan
    - getAge
    - getBiprts
    - getCnnctdNds
    - getDcsd
    - getLvng
    - getNdAge
    - getNdKids
    - getNdLng
    - getNdPD
    - getNdPrdst
    - getNdPrids
    - getNdPtids
    - getNdSlt
    - getNdSstr
    - getNdsAge
    - getNdsFrmTxnyms
    - getNdsKids
    - getNdsLng
    - getNdsPD
    - getNdsPrdst
    - getNdsPrids
    - getNdsPtids
    - getNdsSlt
    - getNdsSstr
    - getOtgrp
    - getPath
    - getPrnt
    - getSpnAge
    - getSpnsAge
    - getSubtree
    - getUnqNds
    - isUltrmtrc
    - list-to-TreeMen
    - loadTreeMan
    - mammals
    - multiPhylo-to-TreeMen
    - phylo-to-TreeMan
    - pinTips
    - plants
    - pstMnp
    - randTree
    - readTree
    - readTrmn
    - rmClade
    - rmNdmtrx
    - rmNodes
    - rmOtherSlt
    - rmTips
    - saveTreeMan
    - searchTxnyms
    - setAge
    - setNdID
    - setNdOther
    - setNdSpn
    - setNdsID
    - setNdsOther
    - setNdsSpn
    - setPD
    - setTxnyms
    - taxaResolve
    - twoer
    - ultrTree
    - unblncdTree
    - updateSlts
    - writeTree
    - writeTrmn
- title: Misc (private)
  desc: Miscellaneous internal functionsuse `phylotaR:::` to access.
  contents:
    - blast_setup
    - download_obj_check
    - safely_connect
    - search_and_cache
    - batcher
    - info
    - error
    - warn
    - blastcache_load
    - blastcache_save
    - sids_check
    - sids_load
    - sids_save
    - cache_rm
    - cache_setup
    - sqs_save
    - ncbicache_load
    - ncbicache_save
    - stages_run
    - stage_args_check
    - mk_txid_in_sq_mtrx
    - obj_check
    - obj_load
    - obj_save
    - summary_phylota
    - parameters_load
    - progress_init
    - progress_read
    - progress_reset
    - progress_save
    - cmdln
    - update_phylota
    - parameters_setup
    - clstrs_save
    - gb_extract
    - rawseqrec_breakdown