v0.4.0

Release notes for v0.4.0

• Renames amsim to knoop. Hip-hip-hooray!
• Fixes critical bug in CMake routine where libaec and libz were dynamically linked dependencies, which means knoop would not run unless those are installed. Existing releases remain broken unless installed in an environment which has these dependencies.
• Refactors core/random.h (formerly core/rng.h) to use Boost's Xoshiro256pp instead of the native Xoshiro256ss random number generator, which is now removed.
• Reworks mating model by adding stall-based termination criterion and adopting sensible default values; --tolerance now controls how far below noise floor the algorithm should aim to be (see below).
• Renames flag --n-threads to --n-workers for compatibility with replicate multithreading (see below).
• Adds benchmarking functionality via Google Benchmark. Some mock benchmarks are implemented in benchmarks/benchmarks.cc and are compiled into the target executable benchmarks.
• Adds support for multithreaded replicate simulations in workers via OpenMP, made available through option --n-threads-per-worker.
• Adds realistic empirical perturbations to spousal correlation objective each generation via generative model; this functionality can be disabled via the new flag --exact.
• Optimises UpdateGenome class by precomputing Bernoulli threshold computation instead of reinvoking at word boundary. This led to significant speedups, making UpdateGenome about as fast as GenerateHaplotypes.
• Adds selection of sample probands via the --include flag; samples can now be customised to only include a select subset of members.
• Adds Doxyfile and a little bit of documentation (will be completed incrementally).
• Renames several files and modules for clarity.

Full Changelog: v0.3.4...v0.4.0

v0.3.4

Release notes

• fix bug in sibling genetic component covariance estimator in #15

Full Changelog: v0.3.3...v0.3.4

Important

Binaries in this release dynamically link libaec and libz and will not launch unless those are installed. This behaviour is fixed in v0.4.0.

v0.3.3

Release notes

• Fixes critical bug in simulations with random mating where same matching was used for the duration of the simulation

Full Changelog: v0.3.2...v0.3.3

Important

Binaries in this release dynamically link libaec and libz and will not launch unless those are installed. This behaviour is fixed in v0.4.0.

v0.3.2

Release notes

• Fixes bug in ancestor covariance estimator which caused crashes for degree > 1
• Fixes annoying behaviour where simulation exits if output directory does not exist; now creates it
• Fixes bug in CI/CD routine to check build status of development branch
• Fixes bug in config writer writing phenotype specs out to phenotypes but reader excepting phenotype

Full Changelog: v0.3.1...v0.3.2

Important

Binaries in this release dynamically link libaec and libz and will not launch unless those are installed. This behaviour is fixed in v0.4.0.

v0.3.1

Release notes

• Adds sibling phenotype covariance estimator accessible via --estimator sibling-cov(<component>) in #12

Full Changelog: v0.3.0...v0.3.1

Important

Binaries in this release dynamically link libaec and libz and will not launch unless those are installed. This behaviour is fixed in v0.4.0.

v0.3.0

Release notes

• Expands mate estimator to include spouse pair siblings and their mates
• Sampling now supports pedigree-based designs
• Adds --no-delete-tmp flag to keep intermediate files
• Fixes bug affecting linux builds

Full Changelog: v0.2.0...v0.3.0

Important

Binaries in this release dynamically link libaec and libz and will not launch unless those are installed. This behaviour is fixed in v0.4.0.

v0.2.0

Important

Binaries in this release dynamically link libaec and libz and will not launch unless those are installed. This behaviour is fixed in v0.4.0.

v0.1.0

Important

Binaries in this release dynamically link libaec and libz and will not launch unless those are installed. This behaviour is fixed in v0.4.0.