The objective of my study is to elucidate the relationship between individual species of mycorrhiza and environmental variables using Spearman correlation. I wonder if I should exclude absences records because not detection doesn't mean inexistence of the specie.... I think that this is true but I am not sure if this is appropriate. What do you think? Is there classical evidence of this topic?
You should not throw good information away. You are acknowledging that your sampling is not perfect but you hope that more mycorrhiza are found if the environment is more favourable. There are a number of approaches that you could use depending on your environmental variables. A place to start could be zero-inflated models. These model both the true absences and the false absences. There should also be some links to suitable methods in the publications below.
Article Occupancy Estimation and Modeling: Inferring Patterns and Dy...
Article Generalized occupancy models allowing false positive and fal...
Thanks a lot Mark, I will read the information! Thank you for your help!
Hello Valeria. Maybe you should also test what is your detection limit by the method you are using to detect them (I guess PCR) to be able to discuss your decision of taking/not-taking them into consideration.
hello, there is not enough ellucidation of your methodology used to study your sample so it is not easy to take position. However when you study AMF, don't forget that some can take up to one year and more before get in symbiosis with the test plant. I think you must be careful while conclude that there is no AMF in your sample
you should also bare in mind that the mycorrhizal fungi may be active or inactive at a given time, they may also be only inside roots (in severe drought external hyphae will be decreased for example) or they may exist as spores in the soil (waiting for right conditions) but not in roots; it's common to find 'different' communities looking at roots or soil.
environmental variables are diverse with precipitation rather than temperature being the most important determinant of fungal symbiosis. your elucidation method should discern root endophytes from AMF. I think mark stanaway's zero inflated model can work but would fail to separate the non-existing from the absences.
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