R Under development (unstable) (2024-05-12 r86534 ucrt) -- "Unsuffered Consequences"
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> # Test data
> # data(varespec)
> testdata <- matrix(round(runif(1000, 0, 100)), nrow=20)
> testdata <- testdata - 50
> testdata[testdata < 0] <- 0
> rownames(testdata) <- paste0("row", seq_len(nrow(testdata)))
> colnames(testdata) <- paste0("col", seq_len(ncol(testdata)))
> 
> # Calculates relative abundance table
> relative <- vegan::decostand(testdata, "total")
> 
> # Count and relative data with pseudocount
> testdata.with.pseudo <- testdata + 1
> relative.with.pseudo <- vegan::decostand(testdata+1, "total")
> 
> # aitchison equals to CLR + Euclid (pseudocount is necessary with clr)
> a1 <- vegan::vegdist(testdata+1, method = "aitchison")
> a2 <- vegan::vegdist(vegan::decostand(testdata+1, "clr"), method = "euclidean")
> max(abs(a1-a2)) < 1e-6 # Tolerance
[1] TRUE
> 
> # Robust aitchison equals to rCLR + Euclid
> # and works without pseudocount
> a1 <- vegan::vegdist(testdata, method = "robust.aitchison")
> a2 <- vegan::vegdist(vegan::decostand(testdata, "rclr"), method = "euclidean")
> max(abs(a1-a2)) < 1e-6 # Tolerance
[1] TRUE
> 
> # Robust aitchison and aitchison are equal when there are no zeroes
> a1 <- vegan::vegdist(testdata.with.pseudo, method = "robust.aitchison")
> a2 <- vegan::vegdist(testdata.with.pseudo, method = "aitchison")
> max(abs(a1-a2)) < 1e-6 # Tolerance
[1] TRUE
> 
> # It is possible to pass pseudocount as a function argument to vegan::decostand
> a1 <- vegan::vegdist(testdata, method = "aitchison", pseudocount=1)
> a2 <- vegan::vegdist(testdata+1, method = "aitchison")
> max(abs(a1-a2)) < 1e-6 # Tolerance
[1] TRUE
> 
> 
> # Compare the outcomes with an external package that also provides compositional transformations
> # Adding these would demand adding Suggested packages in DESCRIPTION; skipped for now but can be
> # useful for manual testing.
> #skip <- TRUE
> #if (!skip) {
> #
> #    sum(compositions::clr(testdata.with.pseudo) - vegan::decostand(testdata.with.pseudo, "clr")) < 1e-6
> #    sum(compositions::clr(testdata.with.pseudo) - vegan::decostand(testdata.with.pseudo, "clr", MARGIN=1)) < 1e-6
> #    sum(t(compositions::clr(t(testdata.with.pseudo))) - vegan::decostand(testdata.with.pseudo, "clr", MARGIN=2)) < 1e-6
> #    sum(rgr::clr(testdata.with.pseudo) - vegan::decostand(testdata.with.pseudo, "clr"))<1e-6#
> #
> #    sum(compositions::alr(testdata.with.pseudo, ivar=1) - vegan::decostand(testdata.with.pseudo, "alr")) < 1e-6
> #    sum(compositions::alr(testdata.with.pseudo, ivar=1) - vegan::decostand(testdata.with.pseudo, "alr", MARGIN=1)) < 1e-6
> #    sum(t(compositions::alr(t(testdata.with.pseudo), ivar=1)) - vegan::decostand(testdata.with.pseudo, "alr", MARGIN=2)) < 1e-6
> #    sum(rgr::alr(testdata.with.pseudo, j=1) - vegan::decostand(testdata.with.pseudo, "alr", reference=1))<1e-6#
> #
> #}
> 
> # --------------------------------------------------------------------------------------------------------------
> 
> 
> proc.time()
   user  system elapsed 
   0.93    0.07    1.01