All notable changes to RcppTskit are documented in this file. The file format is based on Keep a Changelog, and releases adhere to Semantic Versioning.
Added TableCollection R6 class alongside tc_load()
or TableCollection$new(), as well as dump(),
tree_sequence(), and print() methods.
Added TreeSequence$dump_tables() to copy tables into
a TableCollection.
Added TableCollection and reticulate Python round-trip helpers:
TableCollection$r_to_py() and
tc_py_to_r().
Changed the R API to follow tskit Python API for loading:
ts_load(), tc_load(),
TreeSequence$new(), and TableCollection$new()
now use skip_tables and
skip_reference_sequence logical arguments instead of an
integer options bitmask.
Removed user-facing options from
TreeSequence$dump(),
TreeSequence$dump_tables(),
TableCollection$dump(), and
TableCollection$tree_sequence() to match R API with the
tskit Python API, while C++ API has the bitwise options
like the tskit C API.
The bitwise options passed to C++ are now validated.
Used \dontrun{} with get_tskit_py()
calls in examples to further reduce R CMD check time on
CRAN.
Reduced bundled example tree-sequence sizes in
inst/examples/test.trees and
inst/examples/test2.trees to speed up examples and
checks.
Delete temporary files in examples and tests after use.
Renamed unexported functions from
RcppTskit:::ts_load_ptr() to
RcppTskit:::ts_ptr_load() style.
This is the first release.
Initial version of RcppTskit using the tskit C API (1.3.0).
TreeSequence R6 class so R code looks Pythonic.
ts_load() or TreeSequence$new() to load
a tree sequence from file into R.
Methods to summarise a tree sequence and its contents
ts$print(), ts$num_nodes(), etc.
Method to save a tree sequence to a file
ts$dump().
Method to push tree sequence between R and reticulate Python
ts$r_to_py() and ts_py_to_r().
Most methods have an underlying (unexported) C++ function that
works with a pointer to tree sequence object, for example,
RcppTskit:::ts_ptr_load().
All implemented functionality is documented and demonstrated with a vignette.