README.md

In vbonhomme/Modown: A Minimalist Syntax for Morphometrics Data

Modown (in dev.): a minimalist file format for morphometrics data

Rationale

Morphometrics data essentially consist of coordinates and, if any, associated covariates.

Existing morphometrics, eg .tps, .nts, .xml, etc. are not fully generic and/or explicitely defined/consistent, etc.

I propose here the .mod (short for Modown) file format along with R utilities.

Just like markdown, Modown has minimalist syntax and is easy to read/manipulate/write both for humans and machines.

Modown name is derived from markdown, sounds a bit like Momocs and is a tribute to Motown.

Specifications

.mod files are plain text files whose single line syntax fall within one of the five following rules:

1. space-separated numbers stand for coordinates or other numeric data in each dimension: eg -0.5 0.5; 0 0 0
2. word and word/number include a covariate name and its value: eg size 3.14; sp H. sapiens
3. single word introduces a partition of coordinates: eg polygon; points
4. tilde (and word) separate (and name) several individuals in the same file: eg ~; ~iris150
5. anything else is ignored: eg #a comment

Examples

A single shape with one covariate:

name brahma
type beer
37  561
40  540
40  529
[...]

Two shapes with more covariates/cofactors:

~0001-cAglan_O10VD
var Aglan
domes cult
view VD
ind O10
-0.5000 0.00000
-0.4967 0.01035
-0.4935 0.02414
[...]
~0001-cAglan_O10VL 
var Aglan
domes cult
view VL
ind O10
-0.5000 0.00000
-0.4995 0.01018
-0.4957 0.02022
[...]

A single shape with landmarks and 2 partitions of semi-landmarks:

id 571
taxa T. mono
ldk
697  977
766  991
704 1046
[...]
sl1
541 962
542 965
543 967
[...]
sl2
541 949
542 952
542 954
[...]

A shape with nothing else but coordinates:

200   91
187   95
173  105
[...]

Examples adapted from Momocs: bot[1], olea[1], charring[1], shapes[1].

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

vbonhomme/Modown documentation built on May 23, 2019, 3:07 p.m.