bold-deprecated: Deprecated functions in package 'bold'.

In ropensci/bold: Interface to Bold Systems API

Deprecated functions in package bold.

Description

The functions listed below are deprecated and will be defunct in the near future. When possible, alternative functions with similar functionality are also mentioned. Help pages for deprecated functions are available at help("<function>-deprecated").

Usage

bold_identify_parents(
  x,
  wide = FALSE,
  taxid = NULL,
  taxon = NULL,
  tax_rank = NULL,
  tax_division = NULL,
  parentid = NULL,
  parentname = NULL,
  taxonrep = NULL,
  specimenrecords = NULL,
  ...
)

bold_tax_id(
  id,
  dataTypes = "basic",
  includeTree = FALSE,
  response = FALSE,
  ...
)

Details

DEPRECATED. See bold_identify_taxonomy. It's faster and gets the accurate taxonomy directly from the record of the sequence.

This function gets unique set of taxonomic names from the input data.frame, then queries bold_tax_name to get the taxonomic ID, passing it to bold_tax_id to get the parent names, then attaches those to the input data.

Records in the input data that do not have matches for parent names simply get NA values in the added columns.

Value

a list of the same length as the input

bold_identify_parents

For bold_identify_parents, use bold_identify_taxonomy.

Filtering

The parameters taxid, taxon, tax_rank, tax_division, parentid, parentname,taxonrep, and specimenrecords are not used in the search sent to BOLD, but are used in filtering the data down to a subset that is closer to the target you want. For all these parameters, you can use regex strings since we use grep internally to match. Filtering narrows down to the set that matches your query, and removes the rest. The data.frame that we filter on with these parameters internally is the result of a call to the bold_tax_name function.

wide vs long format

When wide = FALSE you get many rows for each record. Essentially, we cbind the taxonomic classification onto the one row from the result of bold_identify, giving as many rows as there are taxa in the taxonomic classification.

When wide = TRUE you get one row for each record - thus the dimensions of the input data stay the same. For this option, we take just the rows for taxonomic ID and name for each taxon in the taxonomic classification, and name the columns by the taxon rank, so you get phylum and phylum_id, and so on.

bold_tax_id

For bold_tax_id, use bold_tax_id2.

References

http://v4.boldsystems.org/index.php/resources/api?type=taxonomy

See Also

bold_tax_name()

Examples

## Not run: 
df <- bold_identify(sequences = sequences$seq2)

# long format
out <- bold_identify_parents(df)
str(out)
head(out[[1]])

# wide format
out <- bold_identify_parents(df, wide = TRUE)
str(out)
head(out[[1]])

x <- bold_seq(taxon = "Satyrium")
out <- bold_identify(c(x[[1]]$sequence, x[[13]]$sequence))
res <- bold_identify_parents(out)
res

x <- bold_seq(taxon = 'Diplura')
out <- bold_identify(vapply(x, "[[", "", "sequence")[1:20])
res <- bold_identify_parents(out)

## End(Not run)
## Not run: 
bold_tax_id(id = 88899)
bold_tax_id(id = 88899, includeTree = TRUE)
bold_tax_id(id = 88899, includeTree = TRUE, dataTypes = "stats")
bold_tax_id(id = c(88899,125295))

## dataTypes parameters
bold_tax_id(id = 88899, dataTypes = "basic")
bold_tax_id(id = 88899, dataTypes = "stats")
bold_tax_id(id = 88899, dataTypes = "images")
bold_tax_id(id = 88899, dataTypes = "geo")
bold_tax_id(id = 88899, dataTypes = "sequencinglabs")
bold_tax_id(id = 88899, dataTypes = "depository")
bold_tax_id(id = c(88899, 125295), dataTypes = "geo")
bold_tax_id(id = c(88899, 125295), dataTypes = "images")

## Passing in NA
bold_tax_id(id = NA)
bold_tax_id(id = c(88899, 125295, NA))

## get http response object only
bold_tax_id(id = 88899, response=TRUE)
bold_tax_id(id = c(88899, 125295), response=TRUE)

## curl debugging
bold_tax_id(id = 88899, verbose = TRUE)

## End(Not run)

ropensci/bold documentation built on Sept. 10, 2023, 11:50 p.m.