# Importing from phyloseq

    if (!requireNamespace("phyloseq", quietly = TRUE)) {
      message("Suggested package: 'phyloseq' is not installed")
      knitr::opts_chunk$set(eval = FALSE)
    } else {
      library(phyloseq)
    }
    library(strollur)

`strollur` includes functionality for the reading and writing of phyloseq objects. To convert a phyloseq object to a strollur object, you need to run the `read_phyloseq()` function.

    # Using the phyloseq example data
    phylo_object <- readRDS(strollur_example("GlobalPatterns.RDS"))
    rdata_object <- read_phyloseq(phylo_object)
    #> Added 19216 sequences.
    #> Assigned 19216 sequence abundances.
    #> Assigned 19216 sequence taxonomies.
    #> Added metadata.
    rdata_object
    #>
    #> Number of unique seqs: 19216
    #> Total number of seqs: 28216678
    #>
    #> Total number of samples: 26
    #> Total number of sequence classifications: 19216
    #> Your dataset includes metadata

Now that are phyloseq object is converted into a strollur object, we can utilize functions like `count()`, `abundance()`, and `names()` to inspect the data.

    count(rdata_object, type = "sample")
    #> [1] 26
    head(names(rdata_object, type = "sequence"))
    #> [1] "549322" "522457" "951"    "244423" "586076" "246140"
    head(abundance(rdata_object, type = "sequence"))
    #>   sequence_name abundance
    #> 1        549322       259
    #> 2        522457         8
    #> 3           951         1
    #> 4        244423        51
    #> 5        586076         3
    #> 6        246140         4

Furthermore, we can output strollur objects as phyloseq objects using the `write_phyloseq()` function.

    phyloseq_object <- write_phyloseq(rdata_object)
    phyloseq_object
    #> phyloseq-class experiment-level object
    #> otu_table()   OTU Table:         [ 19216 taxa and 26 samples ]
    #> sample_data() Sample Data:       [ 26 samples by 7 sample variables ]
    #> tax_table()   Taxonomy Table:    [ 19216 taxa by 7 taxonomic ranks ]
    #> phy_tree()    Phylogenetic Tree: [ 19216 tips and 19215 internal nodes ]

    # With the miseq example data
    miseq <- miseq_sop_example()
    #> Added 2425 sequences.
    #> Assigned 2425 sequence abundances.
    #> Assigned 2425 sequence taxonomies.
    #> Assigned 531 otu bins.
    #> Assigned 2425 asv bins.
    #> Assigned 63 phylotype bins.
    #> Assigned 19 samples to treatments.
    #> Assigned 531 otu bin taxonomies.
    #> Assigned 531 otu bin representative sequences.
    #> Added metadata.
    #> Added 2 resource references.
    #> Added a contigs_report.
    miseq_phyloseq <- write_phyloseq(miseq)
    miseq_phyloseq
    #> phyloseq-class experiment-level object
    #> otu_table()   OTU Table:         [ 2425 taxa and 19 samples ]
    #> sample_data() Sample Data:       [ 19 samples by 2 sample variables ]
    #> tax_table()   Taxonomy Table:    [ 2425 taxa by 6 taxonomic ranks ]
    #> phy_tree()    Phylogenetic Tree: [ 2425 tips and 2424 internal nodes ]