Collapse taxonomy Error in if (class(Tab) != "matrix")

[darioxr]

Since update 4 of R, matrix is now: "matrix" "array", which creates an error

class(Tab)
[1] "matrix" "array"
class(Tab) != "matrix"
[1] FALSE TRUE
Error in if (class(Tab) != "matrix") stop("ERROR: Tab must be a matrix object", :
the condition has length > 1

Could you please update the code to include this new characteristic please. There are some recommendations like changing it to: if (inherits(matrix_obj, "matrix"))
https://stackoverflow.com/questions/64660948/issue-with-creating-a-matrix-in-r

Thanks for your help. I use your package.

Best regards,

DX

[surh]

Thank you for pointing this out. I hadn´t noticed it. It should be fixed now in the latest release.

[darioxr]

Thanks. I installed the new version AMOR_0.2-2. However, I could not find the function "collapse_by_taxonomy.Dataset" or "collapse_by_taxonomy.default". The functions do not appear even when I try AMOR::. Could you please check if there is an installation bug?

[surh]

Thanks, two things:

The first is related to the original issue, while I was checking the collapse_by_taxonomyI realized that it had a similar bug as the original collapse_matrixwhich I had fixed. I also identified and fixed a similar issue with pool_samplesand rarefaction. I think that is all of the instances, but it will take me a few days to confirm so for the moment I´d recommend you install the development version with:

devtools::install_github("surh/AMOR", ref="dev")

This version has all the fixes. Once I confirm there are no lingering issues I will push a new release in the next week or so. I will keep this issue open meanwhile.

Second, about the Dataset & default S3 methods for collapse_by_taxonony. They are available in the package after regular install, it is just that since v 0.1-0 I take full advantage of the S3 utilities. This just means that if you pass a Dataset object to the collapse_by_taxonomy function, R will automatically use the Dataset method, while it will use the default method for everything else. This is the recommended way to use these methods. If for whatever reason you want to force a specific method, you can use the triple colon (i.e. AMOR:::collapse_by_taxonomy.default), but I don´t recommend it.

You can see how the S3 method selection works by running the example from the documentation (copied here):

data(Rhizo)
data(Rhizo.map)
data(Rhizo.tax)

Dat <- create_dataset(Tab = Rhizo, Map = Rhizo.map, Tax = Rhizo.tax)
Dat.phyl <- collapse_by_taxonomy(Dat = Dat, level = 4)

# The followwing returns a matrix
Dat.collapsed1 <- collapse_by_taxonomy(Dat$Tab, Dat$Tax)

# The following returns a dataset object
Dat.collapsed2 <- collapse_by_taxonomy(Dat=Dat)