There are no simliar issues. This is a new feature. The inner_join for treedata will keep the tip or observation from phylo that has a matching key in y.
Example
> tr <- ape::rtree(8)
> x <- data.frame(id = sample(tr$tip.label, 4), trait = rnorm(4))
> tr.da1 <- tr %>% inner_join(x, by=c('label'='id'))
> x2 <- data.frame(id=c('t1', 't1', 't2', 't3', 't2', 't4'), trait=c(10, 20, 30, 40, 50, 60))
> tr.da2 <- tr %>% inner_join(x2, by=c('label'='id'))
> tr.da1
'treedata' S4 object'.
...@ phylo:
Phylogenetic tree with 4 tips and 3 internal nodes.
Tip labels:
t5, t6, t8, t2
Rooted; includes branch lengths.
with the following features available:
'', 'trait'.
# The associated data tibble abstraction: 7 × 4
# The 'node', 'label' and 'isTip' are from the phylo tree.
node label isTip trait
<int> <chr> <lgl> <dbl>
1 1 t5 TRUE 0.478
2 2 t6 TRUE -0.775
3 3 t8 TRUE 0.439
4 4 t2 TRUE 0.962
5 5 NA FALSE NA
6 6 NA FALSE NA
7 7 NA FALSE NA
> tr.da2
'treedata' S4 object'.
...@ phylo:
Phylogenetic tree with 4 tips and 3 internal nodes.
Tip labels:
t4, t3, t2, t1
Rooted; includes branch lengths.
with the following features available:
'', 'trait'.
# The associated data tibble abstraction: 7 × 4
# The 'node', 'label' and 'isTip' are from the phylo tree.
node label isTip trait
<int> <chr> <lgl> <list>
1 1 t4 TRUE <tibble [1 × 1]>
2 2 t3 TRUE <tibble [1 × 1]>
3 3 t2 TRUE <tibble [2 × 1]>
4 4 t1 TRUE <tibble [2 × 1]>
5 5 NA FALSE <NULL>
6 6 NA FALSE <NULL>
7 7 NA FALSE <NULL>
> tr.da2 %>% tidyr::unnest(trait)
# A tbl_df is returned for independent data analysis.
# A tibble: 6 × 4
node label isTip trait
<int> <chr> <lgl> <dbl>
1 1 t4 TRUE 60
2 2 t3 TRUE 40
3 3 t2 TRUE 30
4 3 t2 TRUE 50
5 4 t1 TRUE 10
6 4 t1 TRUE 20
Description
add
inner_joinmethod fortreedataorphyloclassRelated Issue
There are no simliar issues. This is a new feature. The
inner_joinfortreedatawill keep thetiporobservationfromphylothat has a matching key iny.Example