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Hi Brian, When using the mixsiar script with a dataset that has 3 tracers, it produces a biplot of the first 2 tracers but not the third one.
Thanks!
Zou Zou
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1.
``` r
library(ade4)
ord
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I am forever forgetting which way round the scaling numbers go for "site"- or "species"-focussed scalings. The numerical concept for scalings is canonical because of Canoco (& related software) but ev…
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The full taxa strings can be cumbersome to visualize.
An example taxonomy string:
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus;s__
The most informative…
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`qmethod()` currently only returns `zsc` and `zsc_n`, though qfwe() returns `wraw_all`.
For most things Q, it's nice to have only normalized scores (because of the weighing), but sometimes, people mi…
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The taxa vectors aren't being scaled properly in the biplots
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I have run MixSIAR model several times with the same input data. However, the model predictions (such as median (50th percentile) values) were inconsistent. The Gelman diagnostic of some variables wa…
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If you check "Scale coords by percent explained", the arrows in the biplots do not get resized.
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I've been looking at the `biplots.py` code and I'm not understanding the math.
Typically a biplot is generated through a SVD - of course we don't have this luxury since the OTU information is lost wh…