Features for temporal microbiota analysis

[microsud]

Recently, there is an increase in temporal microbiota studies. Addressing relevant analysis such as community turnover, taxa- gain and loss (user defined thresholds for detection), stability of taxa in terms of temporal abundances, as well as reordering of temporally stable (core) taxa will be useful.
Visualisation utilities for community trajectory, taxa ranking through time, etc.
Many of these are used in macroecology, need to check wether specific adaptations are required for microbiota sequencing data. Needs to be done without increasing dependencies for additional libraries.
Open for contributions /suggestions/more features.

[antagomir]

Definitely.

[microsud]

Some analysis is suggested/implemented for macroecological data
References:
Hannah L. Buckley, Nicola J. Day, Bradley S. Case, Gavin Lear, Aaron M. Ellison. Multivariate methods for testing hypotheses of temporal community dynamics

McGeoch, Melodie A., Guillaume Latombe, Nigel R. Andrew, Shinichi Nakagawa, David A. Nipperess, Mariona Roigé, Ezequiel M. Marzinelli et al. "Measuring continuous compositional change using decline and decay in zeta diversity." Ecology 100, no. 11 (2019): e02832.

Lauren M. Hallett, Dan F. B. Flynn, Sydney K. Jones. codyn R package

Collins, Scott L., Katharine N. Suding, Elsa E. Cleland, Michael Batty, Steven C. Pennings, Katherine L. Gross, James B. Grace, Laura Gough, Joe E. Fargione, and Christopher M. Clark. 2008. “Rank Clocks and Plant Community Dynamics.” Article. Ecology 89 (12): 3534–41.

Magurran, Anne E., Maria Dornelas, Faye Moyes, and Peter A. Henderson. "Temporal β diversity—A macroecological perspective." Global Ecology and Biogeography 28, no. 12 (2019): 1949-1960.

We need to see how best to implement/adapt these for micro-ecological data.

For microbiota data:
Guittar, J., Shade, A., & Litchman, E. (2019). Trait-based community assembly and succession of the infant gut microbiome. Nature communications, 10(1), 1-11.

Ji, Brian W., Ravi U. Sheth, Purushottam D. Dixit, Konstantine Tchourine, and Dennis Vitkup. "Macroecological dynamics of gut microbiota." Nature Microbiology 5, no. 5 (2020): 768-775.

For now, I will check these articles. Feel free to add relevant interesting papers.

[antagomir]

Excellent.

[antagomir]

I opened the same issue in TreeSE-based miaTime pkg
microbiome/miaTime#62