Usage
ncbi_taxon_sample(name = NULL, id = NULL, target_rank, min_counts = NULL, max_counts = NULL, interpolate_min = TRUE, interpolate_max = TRUE, min_length = 1, max_length = 10000, min_children = NULL, max_children = NULL, verbose = TRUE, ...)
Arguments
name
(character
of length 1) The taxon to download a sample of sequences for.
id
(character
of length 1) The taxon id to download a sample of sequences for.
target_rank
(character
of length 1) The finest taxonomic rank at which
to sample. The finest rank at which replication occurs. Must be a finer rank than
taxon
. Use get_taxonomy_levels
to see available ranks. min_counts
(named numeric
) The minimum number of sequences to download for each
taxonomic rank. The names correspond to taxonomic ranks.
max_counts
(named numeric
) The maximum number of sequences to download for each
taxonomic rank. The names correspond to taxonomic ranks.
interpolate_min
(logical
) If TRUE
, values supplied to min_counts
and min_children
will be used to infer the values of intermediate ranks not
specified. Linear interpolation between values of spcified ranks will be used to determine
values of unspecified ranks.
interpolate_max
(logical
) If TRUE
, values supplied to max_counts
and max_children
will be used to infer the values of intermediate ranks not
specified. Linear interpolation between values of spcified ranks will be used to determine
values of unspecified ranks.
min_length
(numeric
of length 1) The minimum length of sequences that will be
returned.
max_length
(numeric
of length 1) The maximum length of sequences that will be
returned.
min_children
(named numeric
) The minimum number sub-taxa of taxa for a given
rank must have for its sequences to be searched. The names correspond to taxonomic ranks.
max_children
(named numeric
) The maximum number sub-taxa of taxa for a given
rank must have for its sequences to be searched. The names correspond to taxonomic ranks.
verbose
(logical
) If TRUE
, progress messages will be printed.