rbiom (version 2.2.0)

rbiom-deprecated: Deprecated functions in package rbiom.

Description

The functions listed below are deprecated and will be defunct in the near future. When possible, alternative functions with similar functionality are also mentioned. Help pages for deprecated functions are available at help("<function>-deprecated").

Usage

alpha.div(biom, rarefy = FALSE)
beta.div(
  biom,
  method = "Bray-Curtis",
  weighted = TRUE,
  tree = NULL,
  long = FALSE,
  md = FALSE
)
counts(biom)
info(biom)
metadata(biom, field = NULL, cleanup = FALSE)
nsamples(biom)
ntaxa(biom)
phylogeny(biom)
read.biom(src, tree = "auto", prune = FALSE)
read.fasta(file, ids = NULL)
read.tree(src)
sample.names(biom)
# S3 method for rbiom
select(
  .data,
  samples = NULL,
  nTop = NULL,
  nRandom = NULL,
  seed = 0,
  biom = NULL,
  ...
)
sequences(biom)
subtree(tree, tips)
taxa.names(biom)
taxa.ranks(biom)
taxa.rollup(
  biom,
  rank = "OTU",
  map = NULL,
  lineage = FALSE,
  sparse = FALSE,
  taxa = NULL,
  long = FALSE,
  md = FALSE
)
taxonomy(biom, ranks = NULL, unc = "asis")
tips(x)
unifrac(biom, weighted = TRUE, tree = NULL)
write.biom(biom, file, format = "json")
write.fasta(seqs, outfile = NULL)
write.tree(tree, file = NULL)
write.xlsx(biom, outfile, depth = 0.1, seed = 0)
as.percent(biom)
comments(biom)
depth(biom)
depths_barplot(
  biom,
  rline = TRUE,
  counts = TRUE,
  labels = TRUE,
  transform = "log10",
  ...
)
has.phylogeny(biom)
has.sequences(biom)
id(biom)
is.rarefied(biom)
repair(biom)
sample_subset(x, ...)
sample.sums(biom, long = FALSE, md = FALSE)
taxa_max(biom, rank = -1, lineage = FALSE, unc = "singly")
taxa.means(biom, rank = NULL)
taxa.sums(biom, rank = NULL)
top.taxa(biom, rank = "OTU", n = Inf)
top_taxa(biom, rank = "OTU", n = Inf)
comments(x) <- value
counts(x) <- value
id(x) <- value
metadata(x) <- value
phylogeny(x) <- value
sample.names(x) <- value
sequences(x) <- value
taxa.names(x) <- value
taxa.ranks(x) <- value
taxonomy(x) <- value

<code>alpha.div</code>

Use adiv_matrix() or adiv_table() instead.

<code>beta.div</code>

Use bdiv_table() or bdiv_distmat() instead.

<code>counts</code>

Use $counts instead.

<code>info</code>

Use biom$id, biom$comment, etc instead.

<code>metadata</code>

Use biom$metadata or pull(biom, field) instead.

<code>nsamples</code>

Use biom$n_samples instead.

<code>ntaxa</code>

Use biom$n_otus instead.

<code>phylogeny</code>

Use biom$tree instead.

<code>read.biom</code>

Use as_rbiom() instead.

<code>read.fasta</code>

Use read_fasta() instead.

<code>read.tree</code>

Use read_tree() instead.

<code>sample.names</code>

Use biom$samples instead.

<code>select</code>

Use slice() instead.

<code>sequences</code>

Use biom$sequences instead.

<code>subtree</code>

Use tree_subset() instead.

<code>taxa.names</code>

Use biom$otus instead.

<code>taxa.ranks</code>

Use biom$ranks instead.

<code>taxa.rollup</code>

Use taxa_table() taxa_matrix() instead.

<code>taxonomy</code>

Use $taxonomy instead.

<code>tips</code>

Use tree$tip.label instead.

<code>unifrac</code>

Use bdiv_distmat() or bdiv_table() instead. For weighted=TRUE, returns non-normalized values.

<code>write.biom</code>

Use write_biom() instead.

<code>write.fasta</code>

Use write_fasta() instead.

<code>write.tree</code>

Use write_tree() instead.

<code>write.xlsx</code>

Use write_xlsx() instead.

<code>as.percent</code>

Use biom$counts %<>% rescale_cols() instead.

<code>comments</code>

Use biom$comment instead.

<code>depth</code>

Use sample_sums() instead.

<code>depths_barplot</code>

Use rare_stacked() instead.

<code>has.phylogeny</code>

Use !is.null(biom$tree) instead.

<code>has.sequences</code>

Use !is.null(biom$sequences) instead.

<code>id</code>

Use biom$id instead.

<code>is.rarefied</code>

Use !is.null(biom$depth) instead.

<code>repair</code>

Use as_rbiom(as.list(biom)) instead.

<code>sample_subset</code>

Use biom$metadata %<>% base::subset() instead.

<code>sample.sums</code>

Use sample_sums() or adiv_table() instead.

<code>taxa_max</code>

Use taxa_apply(biom, max, sort = 'desc') instead.

<code>taxa.means</code>

Use taxa_means() instead.

<code>taxa.sums</code>

Use taxa_sums() instead.

<code>top.taxa</code>

Use taxa_sums() instead.

<code>top_taxa</code>

Use taxa_sums() instead.

<code>comments-set</code>

Use biom$comment <- instead.

<code>counts-set</code>

Use biom$counts <- instead.

<code>id-set</code>

Use biom$id <- instead.

<code>metadata-set</code>

Use biom$metadata <- instead.

<code>phylogeny-set</code>

Use biom$tree <- instead.

<code>sample.names-set</code>

Use biom$samples <- instead.

<code>sequences-set</code>

Use biom$sequences <- instead.

<code>taxa.names-set</code>

Use biom$otus <- instead.

<code>taxa.ranks-set</code>

Use biom$ranks <- instead.

<code>taxonomy-set</code>

Use biom$taxonomy <- instead.