Index

A

aic() (in module karenina.fit_timeseries)

apply_perturbation() (karenina.individual.Individual method) apply_perturbation_to_axis() (karenina.individual.Individual method)

B

benchmark_simulated_dataset() (in module karenina.benchmark) benchmark_simulated_datasets() (in module karenina.benchmark)

bm_change() (karenina.process.Process method) bm_update() (karenina.process.Process method)

C

calculate_errors() (in module karenina.benchmark) check_identity() (karenina.individual.Individual method)

check_n_timepoints_is_int() (karenina.experiment.Experiment method) check_perturbation_timepoint() (in module karenina.spatial_ornstein_uhlenbeck) check_variable_specified_per_treatment() (karenina.experiment.Experiment method)

E

ensure_exists() (in module karenina.spatial_ornstein_uhlenbeck)

Experiment (class in karenina.experiment)

F

fit_cohorts() (in module karenina.fit_timeseries) fit_input() (in module karenina.fit_timeseries)

fit_normal() (in module karenina.fit_timeseries) fit_timeseries() (in module karenina.fit_timeseries)

G

gen_output() (in module karenina.fit_timeseries) get_data() (karenina.individual.Individual method)

get_OU_nLogLik() (in module karenina.fit_timeseries) get_timeseries_data() (in module karenina.visualization) graph_absolute_errors() (in module karenina.benchmark)

I

Individual (class in karenina.individual)

is_active() (karenina.perturbation.Perturbation method)

K

karenina.benchmark (module) karenina.experiment (module) karenina.fit_timeseries (module) karenina.individual (module)

karenina.perturbation (module) karenina.process (module) karenina.spatial_ornstein_uhlenbeck (module) karenina.visualization (module)

L

log_lines_from_result_dict() (in module karenina.benchmark)

M

make_OU_objective_fn() (in module karenina.fit_timeseries)

make_OU_objective_fn_cohort() (in module karenina.fit_timeseries) make_scatterplot() (in module karenina.benchmark)

O

ou_change() (karenina.process.Process method)

ou_update() (karenina.process.Process method)

P

parse_metadata() (in module karenina.fit_timeseries) parse_pcoa() (in module karenina.fit_timeseries)

parse_perturbation_file() (in module karenina.spatial_ornstein_uhlenbeck) Perturbation (class in karenina.perturbation) Process (class in karenina.process)

Q

q2_data() (karenina.experiment.Experiment method)

R

random() (in module karenina.individual) remove_perturbation() (karenina.individual.Individual method)

remove_perturbation_from_axis() (karenina.individual.Individual method) run() (karenina.experiment.Experiment method)

S

save_simulation_data() (in module karenina.visualization) save_simulation_figure() (in module karenina.visualization) save_simulation_movie() (in module karenina.visualization)

simulate_movement() (karenina.individual.Individual method) simulate_timestep() (karenina.experiment.Experiment method) simulate_timesteps() (karenina.experiment.Experiment method)

U

update() (karenina.process.Process method) update_3d_plot() (in module karenina.visualization) update_by_addition() (karenina.perturbation.Perturbation method)

update_by_multiplication() (karenina.perturbation.Perturbation method) update_by_replacement() (karenina.perturbation.Perturbation method) update_params() (karenina.perturbation.Perturbation method)

W

write_logfile() (in module karenina.benchmark)

write_options_to_log() (in module karenina.spatial_ornstein_uhlenbeck) write_to_movie_file() (karenina.experiment.Experiment method)