biometrics (version 1.0.3)

assignspp: Assign species botanical information to a data frame

Description

Assigns species botanical attributes to a dataset, based upon a reference column (refcol). The attributes can be any of the fields available in the spplist dataframe, such as: spp.ci.name (genus and epitetus name of the species), spp.name (common name), and spp.ci.abb (abbreviated scientific name).

Usage

assignspp(
  data,
  attri = c("spp.name", "spp.ci.name"),
  refcol = "sppcode",
  all.x = TRUE,
  attri.all = FALSE,
  ...
)

Value

A dataframe object including the attributes defined in the parameter attri.

Arguments

data

A dataframe where to assign the species information.

attri

A string vector having the attributes of the species to be assigned from the species list contained in spplist. This vector, by default, has two attributes: spp.name and spp.ci.name, representing the common name and the scientific name, respectively. Other alternatives are, among others, spp.ci.abb (abbreviated scientific name), genus (genus of the species), and family (family of the species).

refcol

A string having the common column name to be used for linking both the dataset and the species list. In spplist, all the attributes available for the species list are detailed, showing all the information that can be joined to the dataset. Notice that the refcol has to exist in both the dataset and the species list. Additional options of the base::merge() function can be passed to the current assignspp() function.

all.x

Whether to preserve not finded values (TRUE, default) or not (FALSE).

attri.all

By default is set to FALSE, otherwise, will overwrite the vector provided in option attri, with all the attributes available in the species list.

...

Other options for controlling the base::merge() function, which is internally loaded.

See Also

spplist and base::merge().

Examples

## example data frame
myData <- data.frame(narb = c(1, 2, 3),
                     sppcode = c("nob", "np", "nd"),
                     dbh = c(20, 14, 23))
myData


## assign common, scientific and abbreviated name, based on `esp` value (default)
assignspp(myData)

## Assign more than one attribute based on common name
## just to remember, adding a single attribute (different from the default)
assignspp(myData, attri = "spp.ci.name")
## now, a more real example
newData <- assignspp(myData, attri = c("spp.name","genus","spp.ci.abb"))
newData 
## by default this function preserve names not found in biometrics::spplist
missingData <- rbind(myData, c(4, "notFoundData", 30))
missingData
assignspp(missingData, attri = "spp.name")
##the latter can be modified with option `all.x` of the `merge()` function
assignspp(missingData, attri = "spp.name", all.x = FALSE)
## In the case of wanting all the attributes to be merged, set option
## `attri.all` to `TRUE`, which willl overwrite the vector `attri`.
assignspp(missingData, attri = "spp.name", attri.all=TRUE, all.x =
FALSE)