NEWS.md

In mrc-ide/individual: Framework for Specifying and Simulating Individual Based Models

individual 0.1.17

• Add a copy_from method to the Bitset class.
• Improve performance of bitset operations by making num_bits a compile-time constant expression.
• Support vectors of logicals as an argument to filter_bitset.
• Allow processes to be named, in order to produce more useful call stacks.

individual 0.1.16

• Allow events and variables to be added and removed when restoring the simulation.

individual 0.1.15

• Added an all.equal implementation for bitsets.

individual 0.1.14

• Added a flag to the Event constructor to tweak the restore semantics.
• Replaced the Bitset R6 class with named lists, making them faster to instantiate.
• Replaced the bitset sampling implementation with a faster algorithm.
• Various other performance improvements, mostly avoiding copies of vectors.

individual 0.1.13

• Fixed the website generation.
• Fix an uninitialized memory-read that could cause spurious event triggers.

individual 0.1.12

• Simulation state can be saved and restored, allowing the simulation to be resumed.

individual 0.1.11

• Optimised rendering memory usage and speed
• Added benchmarks for rendering

individual 0.1.10

• Vector-based updates are consolidated into one place
• Resizing memory bug fixed
• Simplifed RaggedVariable instantiations to aliases until implementations are implemented

individual 0.1.9

• All variables and targeted events are resizable
• Ragged variables for integers and doubles

individual 0.1.8

• fix bug with C++ event listeners

individual 0.1.7

• Check for bad bitset input when queueing updates to CategoricalVariable objects PR here
• Add "bench" package to suggests and include benchmarking scripts of major functionality in tests/performance PR here
• Update to latest version of "testthat" package so that C++ tests of IterableBitset object can be run without giving LTO check errors (see src/test-bitset.cpp)
• Add CITATION file
• Add method Bitset$clear to zero out all set bits in bitsets PR here
• Fix bug (issue here) where DoubleVariable and IntegerVariable updates could change size of the variable object PR here

individual 0.1.6

• Added a NEWS.md file to track changes to the package.
• Add Mac OS files to .gitignore
• Update pkgdown reference organization.
• Update R-CMD-check workflow.
• Event.h now defines class methods outside of the class definition for easier readability, and add documentation.
• TargetedEvent$schedule now dispatches to different C++ functions in event.cpp and Event.h depending on if input index is a bitset or vector (previous behavior used bitset's $to_vector$ method in R to pass a vector).
• test-event.R now only contains tests for Event class, new test file test-targetedevent.R contains a much updated suite of tests for the TargetedEvent class.
• Fix bug where CategoricalVariable could be queued updates for indices in a vector that were outside the range of the population.
• Update Bitset$not to operate in place. inplace = FALSE will be deprecated in 0.2.0
• Rename the IterableBitset ~ operator to !

individual 0.1.5

• Added package logo.
• Update DESCRIPTION and remove "reshape2" from suggested packages.
• If given a Bitset for argument index, queue_update methods for IntegerVariable and DoubleVariable pass the bitset directly to the C++ functions integer_variable_queue_update_bitset and double_variable_queue_update_bitset rather than converting to vector and using vector methods.
• CategoricalVariable.h, IntegerVariable.h, and DoubleVariable.h now define class methods outside of the class definition for easier readability, and add documentation.
• CategoricalVariable, IntegerVariable, and DoubleVariable classes define a virtual destructor with default implementation.
• get_index_of_set and get_size_of_set_vector methods for IntegerVariable now pass arguments by reference.
• get_values method for IntegerVariable and DoubleVariable corrected to return value rather than reference.
• add overload for get_values for IntegerVariable and DoubleVariable to accept std::vector<size_t> as argument rather than converting to bitset.
• add function bitset_to_vector_internal to IterableBitset.h.
• split testthat/test/test-variables.R into testthat/test/test-categoricalvariable.R, testthat/test/test-integervariable.R, and testthat/test/test-doublevariable.R
• remove unnecessary #include statements from header files.
• remove unnecessary comparisons for size_t types.

mrc-ide/individual documentation built on Aug. 17, 2024, 2:10 p.m.