Function converting template data frame into taxlist object. Also character vectors including taxonomic names will be converted but without any information on taxonomic ranks and parental taxa.
Usage
df2taxlist(x, ...)
# S3 method for data.frame
df2taxlist(x, taxonTraits, taxonViews, levels, clean_strings = TRUE, ...)
# S3 method for character
df2taxlist(x, ...)Arguments
- x
A data frame or a character vector with taxonomic names. If x is a data frame, the columns TaxonUsageID (integer with IDs for each name), TaxonConceptID (integer with IDs for the respective taxon concepts), and TaxonName (character) are mandatory. Other optional columns are AuthorName (character with names' authorities), AcceptedName (logical indicating whether the name is an accepted name or a synonym and will be set as TRUE by default), Level (factor sorting taxonomic ranks in the bottom-up direction), Parent (integer, the taxon concept ID of the parental taxon), and ViewID (integer pointing to the ID of taxonomic view, usually a bibliographic reference, and will be used only if 'taxonViews' is provided. Any further column not included in the prototype of taxlist will be considered as names' attributes and inserted in slot taxonNames.
- ...
Further arguments passed among methods. For the
'character-method', arguments will be passed to the'data.frame-method'.- taxonTraits
A data frame with attributes of taxonomic concepts (optional). If provided, the column TaxonConceptID is mandatorial.
- taxonViews
A data frame or lib_df with references of taxonomic views (optional). If provided, the column ViewID is mandatorial and have to match the homonymous column at 'x'.
- levels
A character vector setting the levels or taxonomic ranks from the bottom to the top. This argument is optional and if missing, the column Level will be preserved (if factor) or coerced to factor, except in the case that no column Level is provided.
- clean_strings
Logical value, whether function
clean_strings()should be applied to 'x' or not.
Value
A taxlist object.
Author
Miguel Alvarez kamapu78@gmail.com.
Examples
Cyperus <- read.csv(file = file.path(path.package("taxlist"), "cyperus",
"names.csv"))
head(Cyperus)
#> TaxonUsageID LETTERCODE SHORTNAME TaxonName NATIVENAME
#> 1 192 CYPEAUR Cyperus auriculatus Cyperus auriculatus NA
#> 2 193 CYPECOR Cyperus corymbosus Cyperus corymbosus NA
#> 3 194 CYPEDIF Cyperus difformis Cyperus difformis NA
#> 4 195 CYPEDIG Cyperus digitatus Cyperus digitatus NA
#> 5 196 CYPEDIS Cyperus distans Cyperus distans NA
#> 6 197 CYPEDIV Cyperus dives Cyperus dives NA
#> AuthorName SYNONYM TaxonConceptID
#> 1 (Nees & Meyen ex Kunth) Kük. FALSE 192
#> 2 Rottb. FALSE 193
#> 3 L. FALSE 194
#> 4 Roxb. FALSE 195
#> 5 L. f. FALSE 196
#> 6 Delile FALSE 197
## Convert to 'taxlist' object
Cyperus$AcceptedName <- !Cyperus$SYNONYM
df2taxlist(Cyperus)
#> object size: 32.1 Kb
#> validation of 'taxlist' object: TRUE
#>
#> number of taxon usage names: 95
#> number of taxon concepts: 42
#> trait entries: 0
#> number of trait variables: 0
#> taxon views: 0
#>
## Create a 'taxlist' object from character vectors
Plants <- df2taxlist(c("Triticum aestivum", "Zea mays"), AuthorName = "L.")
#> Missing column 'TaxonConceptID' in 'x'. All names will be considered as accepted names.
summary(Plants, "all")
#> ------------------------------
#> concept ID: 1
#> view ID: none
#> level: none
#> parent: none
#>
#> # accepted name:
#> 1 Triticum aestivum NA
#> ------------------------------
#> concept ID: 2
#> view ID: none
#> level: none
#> parent: none
#>
#> # accepted name:
#> 2 Zea mays NA
#> ------------------------------