Build a ts
ts_from_dfs.RdBuild a ts
Examples
library(readr)
library(tibble)
subject <- read_csv("https://figshare.com/ndownloader/files/40275934/subject.csv")
#> Rows: 20 Columns: 2
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (2): subject, diet
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
interventions <- read_csv("https://figshare.com/ndownloader/files/40279171/interventions.csv") |>
column_to_rownames("sample")
#> Rows: 236 Columns: 3
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (1): sample
#> dbl (2): Plant, Animal
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
reads <- read_csv("https://figshare.com/ndownloader/files/40279108/reads.csv") |>
column_to_rownames("sample")
#> Rows: 236 Columns: 192
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (1): sample
#> dbl (191): Otu000001, Otu000002, Otu000003, Otu000004, Otu000005, Otu000006,...
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
samples <- read_csv("https://figshare.com/ndownloader/files/40275943/samples.csv")
#> Rows: 236 Columns: 4
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (3): sample, subject, condition
#> dbl (1): time
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ts <- as.matrix(reads) |>
ts_from_dfs(interventions, samples, subject)
#> Joining with `by = join_by(subject)`
ts
#> # A ts_inter object | 191 taxa | 20 subjects | 11.80 ± 3.57 timepoints:
#>
#> Plant5:
#> DD53 DD111 DD24 DD29
#> Otu000001 10.218 9.149 8.392 9.399 …
#> Otu000002 0 0 5.15 8.454 …
#> Otu000003 6.413 0 3.509 3.57 …
#> Otu000004 7.46 6.997 6.855 8.04 …
#> ⋮ ⋮ ⋮ ⋮ ⋱
#>
#> Plant7:
#> DD79 DD34 DD72 DD144
#> Otu000001 9.311 9.368 8.052 9.734 …
#> Otu000002 0 0 4.838 1.844 …
#> Otu000003 7.201 7.575 5.674 7.127 …
#> Otu000004 9.375 9.591 8.313 9.435 …
#> ⋮ ⋮ ⋮ ⋮ ⋱
#>
#> Plant4:
#> DD31 DD146 DD38 DD138
#> Otu000001 8.176 8.512 8.284 8.466 …
#> Otu000002 4.545 0 0 0 …
#> Otu000003 8.471 8.226 7.681 6.527 …
#> Otu000004 0 0 0 0 …
#> ⋮ ⋮ ⋮ ⋮ ⋱
#>
#> and 17 more subjects.