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| Tissue (size_t initial_size=1u, unsigned dimensions=3u, const std::string &coordinate="moore", const std::string &local_density_effect="const", const std::string &displacement_path="random", const EventRates &init_event_rates=EventRates{}, uint_fast32_t seed=std::random_device{}(), bool verbose=false, bool enable_benchmark=false) |
| | Constructor.
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bool | grow (size_t max_size, double max_time=100.0, double snapshot_interval=0.0, size_t recording_early_growth=0u, size_t mutation_timing=0u) |
| | main function
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void | plateau (double time) |
| | Simulate turnover with the increased death_rate.
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void | treatment (double death_prob, size_t num_resistant_cells=3u) |
| | Simulate medical treatment with the increased death_prob.
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std::ostream & | write_history (std::ostream &) const |
| | Write extant_cells_ and their ancestors.
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std::ostream & | write_snapshots (std::ostream &) const |
| | Write snapshots_.
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std::ostream & | write_drivers (std::ostream &) const |
| | Write drivers_.
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std::ostream & | write_benchmark (std::ostream &) const |
| | Write benchmark_.
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std::function< bool(const std::shared_ptr< Cell > &) | insert ) |
| | initialized in init_insert_function()
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std::unordered_set< std::shared_ptr< Cell >, hash_shptr_cell, equal_shptr_cell > | extant_cells_ |
| | cells
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unsigned | id_tail_ = 0 |
| | incremented when a new cell is born
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std::multimap< double, std::shared_ptr< Cell > > | queue_ |
| | event queue
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double | time_ = 0.0 |
| | continuous time
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std::unique_ptr< Coord > | coord_func_ |
| | initialized in init_coord() or init_coord_test()
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std::stringstream | cemetary_ |
| | record dead cells
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std::stringstream | snapshots_ |
| | record snapshots
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std::stringstream | drivers_ |
| | record driver mutations
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std::unordered_set< unsigned > | recorded_ |
| | id of recorded cells
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std::unique_ptr< Benchmark > | benchmark_ |
| | record resource usage
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std::unique_ptr< urbg_t > | engine_ |
| | random number generator
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bool | verbose_ = false |
| | print debug info
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size_t | size () const noexcept |
| | Get the number of extant cells.
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void | init_coord (unsigned dimensions, const std::string &coordinate) |
| | Set coord_func_.
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void | init_insert_function (const std::string &local_density_effect, const std::string &displacement_path) |
| | Set insert function.
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void | migrate (const std::shared_ptr< Cell > &) |
| | Swap with a random neighbor.
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void | push (std::shared_ptr< Cell > moving, const coord_t &direction) |
| | Emplace daughter cell and push other cells to the direction.
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void | push_minimum_drag (std::shared_ptr< Cell > moving) |
| | Push through the minimum drag path.
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void | stroll (std::shared_ptr< Cell > moving, const coord_t &direction) |
| | Try insert_adjacent() on every step in push()
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bool | insert_adjacent (const std::shared_ptr< Cell > &x) |
| | Insert x if any adjacent node is empty.
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bool | swap_existing (std::shared_ptr< Cell > *x) |
| | Put new cell and return existing.
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size_t | steps_to_empty (const coord_t ¤t, const coord_t &direction) const |
| | Count steps to the nearest empty.
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const coord_t & | to_nearest_empty (const coord_t ¤t) const |
| | Direction to the nearest empty.
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coord_t | roulette_direction (const coord_t ¤t) const |
| | Direction is selected with a probability proportional with 1/l.
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uint_fast8_t | num_empty_neighbors (const coord_t &) const |
| | Count adjacent empty sites.
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double | positional_value (const coord_t &) const |
| | TODO: Calculate positional value.
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void | queue_push (const std::shared_ptr< Cell > &, bool surrounded=false) |
| | Push a cell to event queue_.
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void | entomb (const std::shared_ptr< Cell > &) |
| | Put a cell to cemetary_.
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void | snapshots_append () |
| | Write all cells to snapshots_ with time_.
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