docs: Negative time

[RobertJacobsonCDC]

A "Topic" chapter on how to use negative time to have a burn-in period.

[github-actions]

Benchmark Results

Hyperfine

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
large_sir::baseline	3.0 ± 0.0	2.9	3.1	1.00
large_sir::entities	12.3 ± 0.2	12.1	12.7	4.16 ± 0.07

Criterion

Regressions (slower)

Group	Bench	Param	Change	CI Lower	CI Upper
sample_entity	sample_entity_single_property_unindexed	10000	15.117%	14.716%	15.535%
sampling	count_and_sampling_single_known_length_entities		4.224%	3.410%	5.137%
algorithm_benches	algorithm_sampling_multiple_known_length		3.553%	3.047%	4.024%
large_dataset	bench_query_population_multi_unindexed_entities		3.223%	1.507%	4.948%
algorithm_benches	algorithm_sampling_multiple_l_reservoir		3.029%	2.425%	3.597%
sampling	sampling_single_known_length_entities		2.937%	2.158%	3.727%
indexing	query_people_multiple_individually_indexed_properties_entities		2.543%	2.285%	2.950%
sampling	sampling_multiple_l_reservoir_entities		1.950%	1.349%	2.474%
counts	reindex_after_adding_more_entities		1.816%	1.535%	2.144%
sample_entity	sample_entity_multi_property_indexed	10000	1.665%	1.218%	2.029%
sampling	sampling_single_unindexed_entities		1.586%	1.058%	2.087%
sample_entity	sample_entity_multi_property_indexed	100000	1.380%	1.143%	1.604%

Improvements (faster)

Group	Bench	Param	Change	CI Lower	CI Upper
sample_entity	sample_entity_single_property_unindexed	1000	-15.097%	-15.556%	-14.609%
sample_entity	sample_entity_whole_population	10000	-3.616%	-4.041%	-3.320%
examples	example-births-deaths		-2.474%	-3.736%	-1.470%
sample_entity	sample_entity_whole_population	100000	-2.119%	-3.398%	-1.137%
indexing	with_query_results_multiple_individually_indexed_properties_enti		-1.624%	-2.012%	-1.074%

Unchanged / inconclusive (CI crosses 0%)

Group	Bench	Param	Change	CI Lower	CI Upper
algorithm_benches	algorithm_sampling_single_known_length		-1.411%	-2.747%	-0.375%
sample_entity	sample_entity_multi_property_indexed	1000	1.372%	0.812%	2.005%
large_dataset	bench_query_population_property_entities		1.352%	0.122%	2.699%
sample_entity	sample_entity_single_property_indexed	10000	-1.346%	-1.773%	-0.996%
sampling	sampling_single_unindexed_concrete_plus_derived_entities		1.154%	0.930%	1.384%
indexing	query_people_count_indexed_multi-property_entities		0.842%	0.295%	1.392%
counts	multi_property_indexed_entities		-0.701%	-1.215%	-0.018%
counts	index_after_adding_entities		0.684%	0.301%	0.980%
sampling	sampling_multiple_known_length_entities		0.654%	0.005%	1.296%
large_dataset	bench_filter_unindexed_entity		-0.650%	-5.633%	4.530%
counts	concrete_plus_derived_unindexed_entities		0.592%	-0.367%	1.676%
large_dataset	bench_query_population_derived_property_entities		-0.583%	-1.298%	0.120%
sample_entity	sample_entity_whole_population	1000	-0.581%	-1.215%	-0.015%
examples	example-basic-infection		0.454%	-0.391%	1.690%
sampling	count_and_sampling_single_unindexed_concrete_plus_derived_entiti		0.441%	0.223%	0.640%
sample_entity	sample_entity_single_property_indexed	100000	-0.397%	-0.941%	0.024%
large_dataset	bench_query_population_indexed_property_entities		-0.355%	-0.570%	-0.107%
indexing	with_query_results_indexed_multi-property_entities		0.343%	-0.181%	0.862%
algorithm_benches	algorithm_sampling_single_rand_reservoir		0.328%	-0.082%	0.717%
large_dataset	bench_query_population_multi_indexed_entities		0.292%	-0.086%	0.848%
indexing	query_people_single_indexed_property_entities		0.291%	0.143%	0.436%
indexing	query_people_count_single_indexed_property_entities		-0.278%	-0.576%	0.030%
counts	single_property_unindexed_entities		-0.272%	-1.076%	0.469%
counts	single_property_indexed_entities		0.268%	-0.123%	0.775%
sample_entity	sample_entity_single_property_unindexed	100000	0.239%	-0.085%	0.545%
large_dataset	bench_match_entity		-0.225%	-0.556%	0.075%
large_dataset	bench_filter_indexed_entity		0.218%	-11.537%	14.535%
indexing	query_people_indexed_multi-property_entities		-0.141%	-0.480%	0.107%
indexing	with_query_results_single_indexed_property_entities		-0.133%	-0.889%	0.633%
sampling	sampling_single_l_reservoir_entities		0.110%	-1.023%	0.956%
algorithm_benches	algorithm_sampling_single_l_reservoir		-0.093%	-0.248%	0.068%
counts	multi_property_unindexed_entities		0.080%	-0.251%	0.556%
sampling	sampling_multiple_unindexed_entities		0.052%	-0.430%	0.550%
sample_entity	sample_entity_single_property_indexed	1000	0.010%	-0.227%	0.286%
indexing	query_people_count_multiple_individually_indexed_properties_enti		-0.005%	-0.414%	0.279%

[erik-rosenstrom]

I think it looks good and explains the concepts clearly! I think it is an important topic that can be utilized in a number of ways and warrants some coverage in the book.

[k88hudson-cfa]

The concept of initialization v.s. in-simulation time might be good to mention (maybe here, maybe with plans and linking to here)

[github-actions]

Benchmark Results

Hyperfine

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
large_sir::baseline	3.0 ± 0.1	2.9	3.2	1.00
large_sir::entities	12.2 ± 0.3	11.9	13.7	4.03 ± 0.13

Criterion

Regressions (slower)

Group	Bench	Param	Change	CI Lower	CI Upper
sampling	count_and_sampling_single_unindexed_concrete_plus_derived_entiti		5.625%	5.279%	5.976%
sampling	sampling_single_unindexed_concrete_plus_derived_entities		4.886%	4.531%	5.261%
sampling	sampling_multiple_l_reservoir_entities		2.373%	1.772%	2.971%
examples	example-basic-infection		1.880%	1.176%	2.649%
sampling	sampling_multiple_unindexed_entities		1.827%	1.285%	2.363%

Improvements (faster)

Group	Bench	Param	Change	CI Lower	CI Upper
sample_entity	sample_entity_single_property_unindexed	1000	-18.339%	-19.379%	-17.307%
sample_entity	sample_entity_whole_population	100000	-7.083%	-8.063%	-6.240%
indexing	query_people_multiple_individually_indexed_properties_entities		-3.859%	-3.976%	-3.765%
large_dataset	bench_query_population_indexed_property_entities		-3.356%	-4.025%	-2.639%
sampling	sampling_single_l_reservoir_entities		-2.226%	-3.266%	-1.304%
indexing	query_people_count_multiple_individually_indexed_properties_enti		-1.773%	-1.972%	-1.559%

Unchanged / inconclusive (CI crosses 0%)

Group	Bench	Param	Change	CI Lower	CI Upper
large_dataset	bench_filter_indexed_entity		5.599%	-4.306%	16.427%
large_dataset	bench_filter_unindexed_entity		-3.311%	-6.036%	-0.432%
sample_entity	sample_entity_multi_property_indexed	100000	1.523%	0.503%	2.989%
large_dataset	bench_query_population_derived_property_entities		-1.347%	-1.630%	-0.961%
examples	example-births-deaths		1.296%	0.998%	1.574%
counts	multi_property_indexed_entities		0.942%	-0.061%	1.929%
sampling	sampling_single_unindexed_entities		0.814%	0.191%	1.416%
indexing	query_people_count_indexed_multi-property_entities		0.705%	0.307%	1.106%
large_dataset	bench_query_population_multi_indexed_entities		-0.642%	-1.587%	0.224%
sample_entity	sample_entity_multi_property_indexed	10000	0.613%	0.318%	0.867%
indexing	with_query_results_indexed_multi-property_entities		-0.584%	-1.433%	0.129%
algorithm_benches	algorithm_sampling_multiple_known_length		0.552%	0.289%	0.807%
counts	reindex_after_adding_more_entities		-0.461%	-1.019%	0.027%
counts	single_property_indexed_entities		0.429%	0.068%	0.890%
sampling	count_and_sampling_single_known_length_entities		-0.398%	-1.303%	0.503%
counts	single_property_unindexed_entities		-0.397%	-0.867%	-0.062%
large_dataset	bench_query_population_multi_unindexed_entities		0.359%	-0.168%	0.888%
sample_entity	sample_entity_single_property_indexed	1000	-0.359%	-0.857%	0.133%
algorithm_benches	algorithm_sampling_single_rand_reservoir		-0.357%	-0.807%	0.004%
sampling	sampling_multiple_known_length_entities		-0.342%	-1.267%	0.548%
sample_entity	sample_entity_single_property_unindexed	10000	-0.306%	-1.265%	0.640%
large_dataset	bench_query_population_property_entities		0.294%	-0.144%	0.896%
sample_entity	sample_entity_multi_property_indexed	1000	0.268%	-0.024%	0.526%
sample_entity	sample_entity_single_property_unindexed	100000	-0.257%	-0.580%	-0.009%
indexing	with_query_results_multiple_individually_indexed_properties_enti		0.252%	-0.295%	0.679%
algorithm_benches	algorithm_sampling_multiple_l_reservoir		-0.251%	-1.044%	0.433%
indexing	query_people_single_indexed_property_entities		-0.238%	-0.366%	-0.144%
indexing	query_people_count_single_indexed_property_entities		-0.215%	-0.536%	0.025%
algorithm_benches	algorithm_sampling_single_l_reservoir		-0.187%	-0.421%	0.082%
sample_entity	sample_entity_whole_population	1000	0.168%	-0.235%	0.611%
counts	index_after_adding_entities		0.158%	-0.216%	0.514%
sampling	sampling_single_known_length_entities		0.149%	-0.717%	0.898%
sample_entity	sample_entity_single_property_indexed	10000	-0.138%	-0.443%	0.316%
counts	concrete_plus_derived_unindexed_entities		0.095%	-0.320%	0.546%
sample_entity	sample_entity_single_property_indexed	100000	0.093%	-0.400%	0.444%
indexing	query_people_indexed_multi-property_entities		0.080%	-0.052%	0.202%
indexing	with_query_results_single_indexed_property_entities		0.048%	-0.544%	0.695%
algorithm_benches	algorithm_sampling_single_known_length		0.028%	-0.756%	0.750%
sample_entity	sample_entity_whole_population	10000	-0.012%	-0.535%	0.584%
counts	multi_property_unindexed_entities		0.008%	-0.315%	0.318%
large_dataset	bench_match_entity		-0.001%	-0.664%	0.585%