matrix

func (*Matrix) Add ¶

func (m *Matrix) Add(taxon, spec, char, state string)

Add adds a new observation (i.e., a character state) to the matrix for a given taxon specimen, and character.

func (*Matrix) Chars ¶

func (m *Matrix) Chars() []string

Chars returns the characters in the matrix.

func (*Matrix) Obs ¶

func (m *Matrix) Obs(spec, char string) []string

Obs returns the states assigned for character in a specimen.

func (*Matrix) ReadTSV ¶

func (m *Matrix) ReadTSV(r io.Reader) error

ReadTSV reads a set of specimen observations from a TSV file.

The TSV file must contains the following fields:

• taxon, the taxonomic name of the taxon
• specimen, the ID of the particular specimen observed
• character, the name of the observed character
• state, the observed character state

Additional fields are:

• reference, an ID of a bibliographic reference
• image, a path to an image of the observation
• comments, simple comments about the observation

Here is an example file:

# character observations
taxon	specimen	character	state	reference	image	comments
Ascaphidae	ascaphidae:kluge69	tail muscle	present	kluge1969
Ascaphidae	ascaphidae:kluge69	ribs, fusion	free	kluge1969
Discoglossidae	discoglossidae:kluge69	tail muscle	absent	kluge1969
Discoglossidae	discoglossidae:kluge69	ribs, fusion	free	kluge1969
Pipidae	pipidae:kluge69	tail muscle	absent	kluge1969
Pipidae	pipidae:kluge69	ribs, fusion	fused in adults	kluge1969

func (*Matrix) Set ¶

func (m *Matrix) Set(spec, char, state, val string, field Field)

Set sets the value of an addition information for an observation.

func (*Matrix) Specimens ¶

func (m *Matrix) Specimens() []string

Specimens returns the specimens in the matrix.

func (*Matrix) States ¶

func (m *Matrix) States(char string) []string

States returns the states of a character in the matrix.

func (*Matrix) TSV ¶

func (m *Matrix) TSV(w io.Writer) error

TSV writes an observation matrix as a TSV file.

func (*Matrix) Val ¶

func (m *Matrix) Val(spec, char, state string, field Field) string

Val returns the value of additional fields for an observation.