Description Usage Arguments Details Note Examples
This function returns a data frame that contains:
1 2 3 4 5 6 7 | pr2_extract_one_taxo_level(
pr2_taxo,
level_above_name,
level_name,
level_number,
taxo_above
)
|
pr2_taxo |
dataframe - taxonomy with 8 coumns kigdom -> species (but can be more) |
level_above_name |
character - name of the taxo level above (e.g. "order") |
level_name |
character - name the level considered (e.g. "family") |
taxo_above |
dataframe - the same structure than the output of the function but for the level above (e.g. the order if we are the family level) |
name = name of the taxon
taxa_number = number of taxa downstream of this taxon
level = number of the level (e.g. genus = level number 7)
parend_id = id of the first parent taxon (sometimes one taxon has more than one taxon)
id = id of the taxon (just the row name since they are ordered alphabetically )
Here is an example at the genus level name taxa_number level parent_id id Ascampbelliella 1 7 51 1 Choreotrichida_XX 1 7 1 2 Cyttarocylididae_X 1 7 52 3 Cyttarocylis 4 7 52 4 Petalotricha 1 7 52 5 Codonaria 2 7 53 6 Codonella 2 7 53 7
1 | genus_df <- pr2_extract_one_taxo_level(pr2_taxo, "family", "genus", 7, family_df)
|
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