add

Documentation

Overview

Package add implements a command to add taxon ranges to a PhyGeo project.

Index

• Variables

Variables

var Command = &command.Command{
	Usage: `add [-f|--file <range-file>]
	[--type <file-type>] [--format <format>]
	[--filter]
	<project-file> [<range-file>...]`,
	Short: "add taxon ranges to a PhyGeo project",
	Long: `
Command add reads one or more taxon ranges from one or more range files, and
add the ranges to a PhyGeo project. The ranges can be either presence-absence
pixelations, or a continuous range maps.

The first argument of the command is the name of the project file. If no
project exists, a new project will be created.

One or more range files can be given as arguments. If no file is given the
ranges will be read from the standard input. A pixelation model must be
already defined for the project, either a rotation model, or a paleolandscape
model, and the pixelation of the input files must be consistent with that
pixelation model.

By default, only the taxon with ranges defined as presence-absence will be
read. Use the flag --type to define the type of the ranges to be read. The
type can be:

	points	presence-absence taxon ranges
	ranges	continuous range map

By default, the command adds presence-absence files using a tab-delimited
files with the pixel IDs. Using the flag --format, it is possible to define a
different file format. Valid formats are:

	phygeo  the default phygeo format
	darwin  DarwinCore format using tab characters as delimiters (e.g.,
	        the files downloaded from GBIF). Parsed fields are "species",
	        "decimalLatitude", and "decimalLongitude".
	pbdb    Tab-delimited files downloaded from PaleoBiology DataBase, the
	        following fields are required: "accepted_name", "lat", and
	        "lng".
	text    a simple tab-delimited file with the following fields:
	        "species", "latitude", and "longitude".
	csv     the same as text, but using commas as delimiters.

In formats different from the PhyGeo format, all entries are assumed to be
geo-referenced at the present time.

By default, all records in the input files will be added. If the flag --filter
is defined and there are trees in the project, then it will add only the
records that match a taxon name in the trees.

By default the range maps will be stored in the range files currently defined
for the project. If the project does not have a range file, a new one will be
created with the name 'points.tab' for presence-absence taxon ranges, or
'ranges.tab' for continuous range maps. A different file name can be defined
with the flag --file or -f. If this flag is used, and there is a range file
already defined, then a new file will be created, and used as the range file
for the added type of range map for the project (previously defined ranges
will be kept).
	`,
	SetFlags: setFlags,
	Run:      run,
}