Man pages for taxa
Taxonomic Classes

all_functionsGet list of usable functions
all_namesReturn names of data in 'taxonomy()' or 'taxmap()'
arrange_obsSort user data in 'taxmap()' objects
arrange_taxaSort the edge list of 'taxmap()' objects
as_idConvert a vector to database IDs
branchesGet "branch" taxa
can_be_used_in_taxmapCheck that a unknown object can be used with taxmap
check_class_colCheck for name/index in input data
check_for_pkgcheck for packages
check_taxmap_dataCheck dataset format
classificationsGet classifications of taxa
containsdplyr select_helpers
convert_baseConverts decimal numbers to other bases
correct_taxon_namesLook up official names from potentially misspelled names
count_capture_groupsCount capture groups
database_listDatabase list
data_usedGet values of data used in expressions
desc_fontDescription formatting in print methods
ends_withdplyr select_helpers
error_fontFont to indicate an error
everythingdplyr select_helpers
ex_hierarchiesAn example hierarchies object
ex_hierarchy1An example Hierarchy object
ex_hierarchy2An example Hierarchy object
ex_hierarchy3An example Hierarchy object
ex_taxmapAn example taxmap object
ex_taxonomyAn example Taxonomy object
extract_tax_dataExtracts taxonomy info from vectors with regex
filtering-helpersTaxonomic filtering helpers
filter_obsFilter observations with a list of conditions
filter_taxaFilter taxa with a list of conditions
get_dataGet data in a taxmap object by name
get_database_nameReturn name of database
get_data_frameGet data in a taxonomy or taxmap object by name
get_datasetGet a data set from a taxmap object
get_dots_or_listGet input from dots or list
get_sort_varGet a vector from a vector/list/table to be used in mapping
grapes-greater-than-grapesmagrittr forward-pipe operator
hierarchiesMake a set of many 'hierarchy()' class objects
hierarchyThe Hierarchy class
highlight_taxon_idsHighlight taxon ID column
id_classificationsGet ID classifications of taxa
init_taxmap_dataConvert 'data' input for Taxamp
internodesGet "internode" taxa
is_branchTest if taxa are branches
is_internodeTest if taxa are "internodes"
is_leafTest if taxa are leaves
is_rootTest if taxa are roots
is_stemTest if taxa are stems
leavesGet leaf taxa
leaves_applyApply function to leaves of each taxon
length_of_thingCheck length of thing
limited_printPrint a subset of a character vector
lookup_tax_dataConvert one or more data sets to taxmap
map_dataCreate a mapping between two variables
map_data_Create a mapping without NSE
map_uniqueRun a function on unique values of a iterable
matchesdplyr select_helpers
multi_sep_splitLike 'strsplit', but with multiple separators
mutate_obsAdd columns to 'taxmap()' objects
name_fontVariable name formatting in print methods
names_usedGet names of data used in expressions
n_leavesGet number of leaves
n_leaves_1Get number of leaves
n_obsCount observations in 'taxmap()'
n_obs_1Count observation assigned in 'taxmap()'
n_subtaxaGet number of subtaxa
n_subtaxa_1Get number of subtaxa
n_supertaxaGet number of supertaxa
n_supertaxa_1Get number of supertaxa
num_rangedplyr select_helpers
obsGet data indexes associated with taxa
obs_applyApply function to observations per taxon
one_ofdplyr select_helpers
parse_datasetParse options specifying datasets
parse_edge_listConvert a table with an edge list to taxmap
parse_heirarchies_to_taxonomyInfer edge list from hierarchies
parse_possibly_named_logicalused to parse inputs to 'drop_obs' and 'reassign_obs'
parse_raw_heirarchies_to_taxonomyInfer edge list from hierarchies composed of character...
parse_tax_dataConvert one or more data sets to taxmap
pickPick taxa
popPop taxa out
prefixed_printPrint a object with a prefix
print__characterPrint a character
print__data.framePrint a data.frame
print__default_Print method for unsupported
print__factorPrint a factor
print__integerPrint an integer
print_itemPrint a item
print__listPrint a list
print__logicalPrint a logical
print__matrixPrint a matrix
print__numericPrint a numeric
print__orderedPrint a ordered factor
print__tbl_dfPrint a tibble
print_treePrint a text tree
print__vectorGeneric vector printer
progress_lapplylappy with progress bars
punc_fontPunctuation formatting in print methods
ranks_refLookup-table for IDs of taxonomic ranks
remove_redundant_namesRemove redundant parts of taxon names
replace_taxon_idsReplace taxon ids
rootsGet root taxa
sample_frac_obsSample a proportion of observations from 'taxmap()'
sample_frac_taxaSample a proportion of taxa from 'taxonomy()' or 'taxmap()'
sample_n_obsSample n observations from 'taxmap()'
sample_n_taxaSample n taxa from 'taxonomy()' or 'taxmap()'
select_obsSubset columns in a 'taxmap()' object
simplifyList to vector of unique elements
spanSpan taxa
starts_withdplyr select_helpers
stemsGet stem taxa
subtaxaGet subtaxa
subtaxa_applyApply function to subtaxa of each taxon
supertaxaGet all supertaxa of a taxon
supertaxa_applyApply function to supertaxa of each taxon
taxaA class for multiple taxon objects
taxmapTaxmap class
taxonTaxon class
taxon_databaseTaxonomy database class
taxon_idTaxon ID class
taxon_idsGet taxon IDs
taxon_indexesGet taxon indexes
taxon_nameTaxon name class
taxon_namesGet taxon names
taxonomyTaxonomy class
taxonomy_tableConvert taxonomy info to a table
taxon_rankTaxon rank class
taxon_ranksGet taxon ranks
tid_fontTaxon id formatting in print methods
to_percentFormat a proportion as a printed percent
transmute_obsReplace columns in 'taxmap()' objects
unique_mappingGet indexes of a unique set of the input
validate_regex_key_pairCheck a regex-key pair
validate_regex_matchCheck that all match input
validate_taxmap_funcsValidate 'funcs' input for Taxamp
taxa documentation built on April 30, 2020, 1:05 a.m.