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MoBiodiv / mobr

Tools for analyzing changes in diversity across scales
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How to incorporate blocks or strata into the mob delta analysis #129

Open dmcglinn opened 7 years ago

dmcglinn commented 7 years ago

Currently in the delta analysis all of the plots in a given treatment are as part of the same "population" but many times in experimental designs there are blocks that the investigator would like to be able to control for when carrying out the analysis of the treatment effect. This same problem also occurs in analyses of time series such as in the Portal dataset in which there are many plots in the same treatment that each have been sampled through time. If one is only interested in temporal (rather than spatial) patterns of species accumulation then a method is needed to be able to average across the individual quadrat results for both the observed and null deviations.

My feeling is that the way we want to approach this is to estimate the treatment level curve by averaging the separate block specific curves, but in practice this may be difficult to implement because some blocks may have small sample sizes (individuals or samples) and because all of how our null models are conducted. Let's use this thread to brainstorm how to best implement these analyses

rueuntal commented 7 years ago

I'm no expert in experiment design so this could be completely out of the line - would be problematic if plots within a block are simply lumped?

dmcglinn commented 7 years ago

Yes I think this is what we must do is sample across plots within a block (i.e., lump them), but its when it is the plots between blocks that it is less clear what to do.

On Wed, Feb 15, 2017 at 3:25 PM, Xiao Xiao notifications@github.com wrote:

I'm no expert in experiment design so this could be completely out of the line - would be problematic if plots within a block are simply lumped?

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dmcglinn commented 7 years ago

For the boxplot analysis where we use permutation based significance tests we could using the permute package to allow for permutations within strata:

plots = Plots(strata = gl(3, 4))
CTRL = how(plots = plots, within = Within(type = 'free'))
shuffle(3 * 4, CTRL)