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To download tRophicPosition package visit https://github.com/clquezada/tRophicPosition
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Dear Claudio,Thank you for your prompt reply and your work on this great package.I could plot the data using the package plot function for both my dataset and the package dataset.For the test_data1, the multiSpeciesTP function had run for 30 min then an error come out.Attached with the data and the scripts I used for my data and the package data.As my real data actually contains far more species, it would be great if I can run the multi species in parallel. Thank you for your help in advance.Best Regards,Jason
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Dear Claudio,All the things work well with your script provided. Thanks a lot.#About minmum sample sizeMay I know the minimum sample size that you recommended for calculating TP using the package? Or does it actually depends on the variance of the isotopic signature? I asked because we have too many species to process and isotope analysis of each sample is quite expensive so we decide to have as few samples as possible to minimise the cost.
#About baselineRegarding to the baseline, I actually group all the bivalvia species and the filter feeding gastropod as one baseline with the assumption that all of the bivalvia species are filter feeding species. I do this because I don’t actually have much information on the bivalve feeding ecology and also none of the bivalve species occurred in all site and season. Do you think this grouping is reasonable when using the package? Or is there any better way for setting the baseline?
#About check the quality of the estimateLast question is about how to check the accuracy of the estimate. In your recently published paper, it mentioned to look at the plot generated from the CODA package. There are 4 panels from the plot, I assume the density plot is to check the normality of the TP and muDeltaN where trace plot is to check for convergence. If the trace plot didn’t look flat but contain multipeaks then it would be regarded as not converging [Attached Figure]? Besides increase the sample size, what else can we do to obtain a reliable estimate based on the data we have? For the muDeltaN, as long as I am using the TDF either from McCutchan or Post assumption, it will be okay?
I am sorry for asking so many questions as I am really new to bayesian statistics.Best Regards,Jason
On 11 Apr 2018, at 9:34 AM, Claudio Quezada R. <clqu...@ug.uchile.cl> wrote:
Dear JasonI found the plot problem: in the vignette there was an error. Thank you for pointing this out. You should use
credibilityIntervals(Bilagay_models$df, x = "group", xlab ="Community")instead of using x = "community"Regarding your data, I strongly suggest to check every species/consumer in every site/community/group, as you have some combinations of species/groups that don't have enough data, and the estimation of trophic position will be skewed and might not be reliable.
For example, Sp4 in Wet-SE has only 4 stable isotope values! And the baseline Pelagic_BL doesn't seem to be good too.
<Sp4 Wet-SE.jpeg>
If you calculate TP, you will see that the trace of TP is clearly not smooth, which suggests that the data is poor and the model is not converging successfully. Still you will have results, but they might be skewed or probably wrong. Posterior distribution of trophic position range from 2 to 9? That is not a good sign.
<trace Sp4 Wet-SE.jpeg>
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<test_script.R>