momx / momfarm Goto Github PK

Part of MomX

None of what follows will be ready before end of April 2020 !!!

MomX is an ecosystem of R packages for everything 2D morphometrics, that is the statistical description of shape and its (co)variation.

MomX is intended to provide a complete, comfortable, powerful, and - last but not least - open-source workflow for morphometrics.

MomX packages share common principles and work together well. This architecture is largely inspired by the tidyverse.

1. Finish rewriting Momocs, release (April 2020)
2. Port old Momocs stats to Momcalc, release (April 2020)
3. Finish Momit, release (May 2020)
4. Finish MomX, release (May 2020)
5. Finish Momacs and Momoshop, release (June 2020)
6. Submit to rOpenSci

Import from various image and foreing file format and defines a portable format for morphometrics data

Momit website

Interactively acquire morphometrics data from images, eg defining landmarks, curves, and other regions of interest.

Momacs website

Post-processes images, eg adjust contrast, pick channels, remove background, etc.

Momoshop website

Manipulating shapes and turning them into coefficients using morphometrics methods.

Momocs2 website

Wraps sensible statistics methods for morphometrics in a consistent grammar

Momstats website

Is the shiny descent of Momocs x Momecs

Momecs website

Install and manage all MomX packages

MomX website

Interesting datasets for MomX

Momdata website

Compiles all package documentation into a practical book for MomX

Share and archive morphometrics data

• MomX aims to be a complete and user-friendly ecosystem for morphometrics
• Compartiment key processes into well-defined, interoperable packages that go together well.
• Each package should solve a single task, and do it well. Make it work, document, release, improve, repeat.

MomX embraces and owns much to the tidy manifesto. MomX kind of theorise the programming side of morphometrics, or at least itself (yes, infinite loop). Tibbles are the answer.

MomX packages share :

• Continous integration with Travis
• Continuous testing with [pkg::testthat] and codecov
• Companion website built by [pkg::pkgdown], at url: MomX.github.io/packagename
• Cheatsheets to decorate your bathroom walls

Will come on top when ready

Once on CRAN, install the last released version of a package, say “MomX” with:

install.packages("MomX")

I will typically only support the very last development versions that you can get from GitHub with:

# install.packages("devtools")
devtools::install_github("MomX/MomX")

Then you will need to laod it with :

library(MomX)

You can install and use packages separetely (eg with install.packages("Momocs"). MomX package will install all MomX packages, and help update them.

I’m much than welcoming contributions to MomX ! Good news is that whatever your skills, you can contribute a bit.

You can :

• Signal a bug : fill an issue with bug label 🐛
• Code, improve, develop, discuss, request new features : fill an issue with discuss 🔧
• Improve examples, and my English : edit pages 🇬🇧

I do not have time either, so before asking for help, please :

• Make sure you have the very last versions of packages : MomX::MomX_update
• Start reading the vignettes, they are a good place to start 📚
• Read the reference manual, understand examples 🐣
• Go to walk for 2 hours in the forest 🌳 🐗 🍀, solves 95% of my problems
• Show us what you have tried and make a reproducible example 💊

Then, if you think something is wrong with :

• is wrong with MomX : fill an issue with bug
• is wrong with you, your data, or something local, fill an issue tagged with help

Feel free to ring my bell <[email protected]> if :

• You would like to collaborate with me
• You would like to get trained in R and/or MomX
• Any other sensible reason

Happy MomX-ing 😘 !