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A function to construct a LifemapR object, usable by the other functions of the package.

Source: R/build_Lifemap.R
build_Lifemap.Rd

A function to construct a LifemapR object, usable by the other functions of the package.

Usage

build_Lifemap(df, basemap = NULL, verbose = TRUE)

Arguments

df

A dataframe containing at least one column named "taxid" that contains NCBI Taxonomy Identifiers (taxid). The dataframe can contain any number of additional columns defining traits/characters/values associated to each taxid.

basemap

Deprecated argument.

verbose

If TRUE (the default), the function will print detailed information to the console. If FALSE, it will run silently.

Value

A list of class lifemap_obj containing:

  • df : a dataframe containing at least for each taxid :

    • The x coordinate (lon)

    • The y coordonate (lat)

    • The scientific name (sci_name)

    • The zoom level at which the taxa is visible (zoom)

    • A list of its ascendants (ascend)

    • Its type ("requested" or "ancestor")

    • Its direct ancestor

    • Its type (type), i.e. whether the taxid was requested by the user ("requested") or if it is the anecestor of a requested taxid ("ancestor")

  • basemap : the basemap used to get taxa's details

Examples

data(eukaryotes_80)
if (FALSE) { # \dontrun{
# make sure you have a good internet connection to load these very large files
LM <- build_Lifemap(eukaryotes_80)
} # }