Thanks for providing this package.

Following your advice, I plan to run alphawichVis to see the differences for determining the repeated iterations. I tried to use example date at first, but I met a problem when I ran the code alphawichVis(example, "Id"). The "R session Error" occurs, showing "The previous R session was abnormally terminated due to an unexpected crash".

Here is the full code.

library(mirlyn)
data(example)
example1 <- mirl(example, rep = 100)
example2 <- alphadivDF(example1)
alphawichVis(example2, "Id")

Looking forward to your reply. Thanks!

Viven

Thanks so much for creating and maintaining this package!

I am wondering what diversity metric is being calculated for Alpha diversity? The graph just says "Diversity Index" and the paper mentions both Shannon Index and Hill Number. Is there a way to specify what metric we want?
Sorry if this is already in the docs and I missed it.

HPC sites prefer properly released versions.

Hi! First, thank you for creating this package, it is really helpful. I was wondering if I could ask for your help with the following. I just rarefied my data using the function mirl, and now I would like to transform the resulting mirl object back to a phyloseq object. There are a few steps in my downstream analysis that I can not do using the mirl object (i.e. permanova test, beta diversity with unifrac distances, etc). Would you be able to explain to me how to transform the mirl object back to a phyloseq object? I am wondering if i could get an average of the iterations for each observed ASV, if possible.

Dear mirlyn developers,

First of all I would like to congratulate you for the mirlyn R package and the concept of rarefaction multi-iterative.

I know that the R package is in the initial phase, but I would like to replicate Figure 4 and Figure S1,I of your original manuscript: Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities. but I am not capable.

I realised that alphacone() and alphadivDF() functions contain the diversity argument but I don't find the argument to choose between replacement or not.

And also for the abovementioned figures of your manuscript: I understand that is not possible to obtain from mirlyn R package. or yes? I understand that you have been customized it and you have analized separately at library size at 500, 1000, 5000 and 11213. And how you ploted the observed situation?

Thanks on advance for your hints/comments,
Magi.

When trying to plot rarefaction curves, the function rarecurve() brings up the error:

Error in round(x): non-numeric argument to mathematical function

I explored the stack trace for a while and I don't get what the round() function is used for, I suppose it serves the purpose of checking that the sample names provided are just ordinal numbers and integers, but even when I use a mock column with just integers in it, it doesn't work.

Hi, thanks very much for creating this package!

I'm having a few problems running the example code:

• The code to visualize alpha diversity, alphawichVis(example, xvar = "Sample") didn't work for me. Although I think I managed to produce the intended plot with alphawichVis(alphadiv_df, xvar = "Id").
• I was able to create a dataframe of alpha-diversity metric across all library sizes using alphacone, but the plotting code, alphaconeVis(alphacone_example, "Sample"), did not work for me. The error was Error: geom_ribbon requires the following missing aesthetics: x or y, xmin and xmax.
• The code for visualizing the PCA is missing a quotation mark around the grouping variable name "F". But otherwise it worked fine.

I'm also wondering whether it is possible to use multiple cores when running the mirl function?

Thanks again, this is a very helpful package.

Laura

I used the 'mirl' function on my phyloseq object named ps05
mirl_ps05 <- mirl::mirl(ps05, libsize = 1000, rep = 100, set.seed = 120)
To create a mirl object.
Examining the mirl object I can see it holds:
A list of 100 phyloseq objects, where each phyloseq object contains:
otu table [7212 * 237]
tax table [7212 * 27]
sam data [237 * 22]

I now wish to use the 'betamatPCA' function . Perhaps like this:

betamatPCA_ps05 <- mirlyn::betamatPCA(mirl_ps05, dsim = "bray")

But this appears to be impossible on my computer. Rstudio continues to crash.
I assume this happens because the PCA analysis I am requesting is too heavy.

Do you have any good advice on how to proceed with the 'betamatPCA' when the phyloseq object is very large?
I guess it will end up being a common issue since DNA metabarcoding very often ends up with very large otu tables and very large tax tables.

My otu, tax and sam tables can be obtained from these dropbox weblinks
https://www.dropbox.com/scl/fi/lck08gsme1b3kiqyyl8en/table_df_tax05.csv?rlkey=n5c1qny7tdrm39la6eb42tiz0&dl=0
https://www.dropbox.com/scl/fi/r4okjl5mefg54cvixdcvt/table_df_sam05.csv?rlkey=t0trgzi77jybreslsnnvial2p&dl=0
https://www.dropbox.com/scl/fi/w3emynu0ohor0iynpcfkw/table_df_otu05.csv?rlkey=gv4g4eo7z5nj10bk2w2bzc6k7&dl=0

I was using the get_asv_table function and the warning was displayed:
'Warning message:
funs() was deprecated in dplyr 0.8.0.
i Please use a list of either functions or lambdas:

Simple named list: list(mean = mean, median = median)

Auto named with tibble::lst(): tibble::lst(mean, median)

Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))

i The deprecated feature was likely used in the mirlyn package.
Please report the issue to the authors.
This warning is displayed once every 8 hours.
Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.'

Hi,

First of all, this is a great package! Thank you very much.

Since the recent update of mirl() to V1.4.1, I am not able to run phyloseq objects as x in the function.
Using the example data from mirlyn:

data("example")
example

phyloseq-class experiment-level object
otu_table() OTU Table: [ 3342 taxa and 6 samples ]
sample_data() Sample Data: [ 6 samples by 1 sample variables ]
tax_table() Taxonomy Table: [ 3342 taxa by 7 taxonomic ranks ]
phy_tree() Phylogenetic Tree: [ 3342 tips and 3336 internal nodes ]

mirlps <- mirl(example, rep = 5)

Error in if (ncol(x) > ncol(mirlobj[[1]])) { : argument is of length zero

It seems to work fine with just an otu table, but I'm no longer able to run mirl() on a phyloseq object.