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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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.