Dear, I’ve got a experimental mesocosm dataset with 2 groups (control x treatment) over 4 different sampling time (0h, 24h, 72h and 120h) and I wanna know if there is a difference between that groups over the time. So, I’ve applied PERMANOVA to evaluate the statistical difference and both factors (condition and time) have contributed to the difference … However I’d like to know a possibility to get which OTUs were different.
Besides that, I’ve also got some physico-chemical parameters such as temperature, pH, dissolved O2, organic matter, nitrate, nitrite, phosphorus, turbidity, etc etc and I’d like to know if I can apply a statistical function to know which of these parameters were different over the time (I also know according to PERMANOVA there is a difference between condition x time but I don’t know which of them were different).
figuring out which OTUs are different isn’t a simple task. a few of the tools that I have used:
indicator species analysis (indicspecies R package)
lefse (lefse R package)
LDA (through galaxy, not sure of R package)
glmm (mvabund R package)
There have been a few timeseries specific tools coming out recently but I haven’t had a chance to try them yet
I haven’t used simper in a long time, but off the top of my head I can’t remember why. sorry, I know I compared it (and anosim and mrpp) to permanova (combined with indicator species) and chose permanova/indicspecies. At the time I was working with a giagantic forest soils dataset, so it could be that simper couldn’t handle the data or there was a bias in simper I didn’t like.