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Bio-Community-0.001006
River stage zero No dependents
1 ++

Changes for version 0.1.6 - 2014-04-29

  • New script, bc_manage_members, to rename and remove given community members
  • Added new richness estimators to Bio::Community::Gamma: Chao-2 (suggested by Renato Santos), ICE and jackknife (first & second-order)
  • Added first and second-order jackknife estimators to Bio::Community::Alpha
  • ACE estimator of richness now falls back to Chao-1 in special case (as advised by Anne Chao and implemented in EstimateS)

Documentation

bc_add_taxonomy
Add a taxonomic lineage to community members
bc_clean_shrapnel
Remove low-count, low-prevalence community members
bc_convert_files
Merge/split community files and convert between formats
bc_convert_ids
Convert member ID from member attribute or file
bc_correct_mis_assignments
Try fixing incorrect taxonomic assignments, using a reference community
bc_get_info
Get information about a community file
bc_manage_members
Delete or rename community members
bc_manage_samples
Include, delete, merge, sort or rename samples
bc_measure_alpha
Measure alpha diversity of communities
bc_measure_beta
Measure beta diversity between communities
bc_rarefy
Rarefy communities
bc_relative_to_absolute
Convert relative abundances into absolute
bc_remove_unexpected_members
Remove community members not expected to occur, based on a reference community
bc_summarize
Summarize community composition

Modules

Bio::Community
A biological community
Bio::Community::Alpha
Calculate the alpha diversity of a community
Bio::Community::IO
Read and write files that describe communities
Bio::Community::IO::Driver::biom
Driver to read and write files in the sparse BIOM format
Bio::Community::IO::Driver::dummy
Dummy driver (does nothing)
Bio::Community::IO::Driver::gaas
Driver to read and write files in the GAAS format
Bio::Community::IO::Driver::generic
Driver to read and write files in a generic tab-delimited site-by-species table format
Bio::Community::IO::Driver::qiime
Driver to read and write files in the QIIME format
Bio::Community::IO::Driver::unifrac
Driver to read and write files in the (Fast)Unifrac format
Bio::Community::IO::FormatGuesser
Determine the format used by a community file
Bio::Community::Member
The basic constituent of a biological community
Bio::Community::Meta
A metacommunity, or group of communities
Bio::Community::Meta::Beta
Beta diversity or distance separating communities
Bio::Community::Meta::Gamma
Calculate the gamma diversity of a metacommunity
Bio::Community::Role::Classified
Role for objects that have a taxonomic classification
Bio::Community::Role::Described
Role for objects that have a description
Bio::Community::Role::IO
Role for IO layer
Bio::Community::Role::Locked
Role for objects that can be locked (made read-only)
Bio::Community::Role::PRNG
Role for objects that use a pseudo-random number generator
Bio::Community::Role::Sequenced
Role for objects that have a sequence
Bio::Community::Role::Table
Role to read/write data tables and provide random access to their cells
Bio::Community::Role::Weighted
Role for objects that have a weight
Bio::Community::TaxonomyUtils
Functions for manipulating taxonomic lineages
Bio::Community::Tools::IdConverter
Various methods to convert member ID
Bio::Community::Tools::Rarefier
Normalize communities by count
Bio::Community::Tools::Sampler
Sample organisms according to their abundance
Bio::Community::Tools::ShrapnelCleaner
Remove low-count, low-abundance community members
Bio::Community::Tools::Summarizer
Create a summary of communities
Bio::Community::Tools::Transformer
Arbitrary transformation of member counts
Bio::Community::Types
Data type definitions

Other files