Rtskit

Rtskit is a native R interface to succinct tree sequences through the stable tskit C API. It does not use Python, reticulate, Rust, Java, or a system tskit shared library.

The initial interface keeps each tsk_treeseq_t under one native external pointer and exposes deliberate materialization operations for summaries, sample nodes, node, edge, population, and individual tables, opaque metadata bytes, tree intervals, and source-population ancestry intervals.

Install the development build from R-universe:

install.packages(
  "Rtskit",
  repos = c(
    RGenomicsETL = "https://rgenomicsetl.r-universe.dev",
    CRAN = "https://cloud.r-project.org"
  )
)

library(Rtskit)

trees <- tskit_example()
trees

## <Rtskit::TreeSequence>
##   source: <memory>
##   sequence length: 10
##   trees: 2
##   samples: 2

tskit_nodes(trees)

##   id flags time population individual
## 1  0     1    0         -1          0
## 2  1     1    0         -1          0
## 3  2     0    1          0         -1
## 4  3     0    1          1         -1

tskit_edges(trees)

##   id left right parent child
## 1  0    0     5      2     0
## 2  1    0     5      2     1
## 3  2    5    10      3     0
## 4  3    5    10      3     1

tskit_trees(trees)

##   index left right roots edges
## 1     0    0     5     1     2
## 2     1    5    10     1     2

tskit_ancestry_intervals(
  trees,
  c("panel:source_A" = 0L, "panel:source_B" = 1L)
)

##   sample left right         source source_population
## 1      0    0     5 panel:source_A                 0
## 2      0    5    10 panel:source_B                 1
## 3      1    0     5 panel:source_A                 0
## 4      1    5    10 panel:source_B                 1

IDs retain tskit’s zero-based indexing. tskit_metadata() and tskit_metadata_schema() return exact raw bytes: decoding remains an explicit caller decision because the C API does not itself interpret metadata codecs. Source-population ancestry is valid only when the simulation provenance makes its retained node populations authoritative.

Native ownership

• TreeSequence owns one initialized tsk_treeseq_t.
• The external-pointer finalizer calls tsk_treeseq_free() exactly once.
• Native table memory is borrowed only for the duration of a .Call().
• R data frames are copies requested explicitly by the user.
• Invalid or finalized pointers fail before native access.

Vendored authority

The source package statically compiles tskit C API 1.3.1 and kastore 2.1.2 from tskit tag 1.0.3, commit b62f75f04af81fbf5f0d6fb38953cb97b587737f. One audited host-integration patch routes impossible native invariant failures through an R error instead of terminating the process. tools/upstream.json, the complete manifests, and patches/check.sh prove the downstream source reconstructs the pin exactly.

Rtskit is GPL-2 or later. The bundled tskit and kastore sources retain their MIT licences and copyright notices.