SLIM
v0.2.1
Contents:
Introduction
Getting Started
Model Overview
Configuration
Development guide:
Testing
slim
SLIM
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Index
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
A
add_busy_dams_batch() (slim.simulation.lice_population.LicePopulation method)
add_treatment() (slim.simulation.farm.Farm method)
addSmoothedPlot() (slim.gui_utils.plots.SmoothedGraphicsLayoutWidget method)
affecting_date (slim.types.QueueTypes.TreatmentEvent attribute)
aggregation_rate (slim.simulation.cage.Cage property)
Allele (in module slim.simulation.lice_population)
allele_labels (slim.simulation.lice_population.GenoDistrib attribute)
alleles (slim.simulation.lice_population.GenoDistrib attribute)
annealing() (slim.Optimiser.Optimiser method)
arrival_date (slim.types.QueueTypes.TravellingEggBatch attribute)
as_dict() (slim.simulation.lice_population.LicePopulation method)
ask_for_treatment() (slim.simulation.farm.Farm method)
availability_date (slim.types.QueueTypes.DamAvailabilityBatch attribute)
available_dams (slim.simulation.lice_population.LicePopulation property)
average_fish_mass() (slim.simulation.cage.Cage method)
B
batch_sum() (slim.simulation.lice_population.GenoDistrib static method)
busy_dams (slim.simulation.lice_population.LicePopulation property)
C
Cage (class in slim.simulation.cage)
CageEvent (class in slim.types.QueueTypes)
cfg (slim.gui_utils.model.SimulatorSingleRunState attribute)
ChemicalTreatment (class in slim.types.TreatmentTypes)
cleanPlot() (slim.gui_utils.plots.SingleRunPlotPane method)
clear() (slim.gui_utils.console.ConsoleWidget method)
clear_busy_dams() (slim.simulation.lice_population.LicePopulation method)
clear_log() (slim.LoggableMixin method)
color_palette (slim.gui_utils.plots.SmoothedPlotItemWrap attribute)
compute_eta_aldrin() (slim.simulation.cage.Cage method)
Config (class in slim.simulation.config)
ConfigurationPane (class in slim.gui_utils.configuration)
ConsoleWidget (class in slim.gui_utils.console)
copy() (slim.simulation.lice_population.GenoDistrib method)
create_logger() (in module slim)
create_offspring() (slim.simulation.cage.Cage method)
CurveListState (class in slim.gui_utils.model)
CustomFarmEncoder (class in slim.JSONEncoders)
D
DamAvailabilityBatch (class in slim.types.QueueTypes)
default() (slim.JSONEncoders.CustomFarmEncoder method)
delay() (slim.types.TreatmentTypes.EMB method)
(slim.types.TreatmentTypes.Thermolicer method)
(slim.types.TreatmentTypes.TreatmentParams method)
deleteLater() (slim.gui_utils.plots.SmoothedGraphicsLayoutWidget method)
detected_rate (slim.types.QueueTypes.SamplingResponse attribute)
disconnectAll() (slim.gui_utils.plots.SmoothedGraphicsLayoutWidget method)
DISCRETE (slim.types.TreatmentTypes.GeneticMechanism attribute)
disperse_offspring() (slim.simulation.farm.Farm method)
do_infection_events() (slim.simulation.cage.Cage method)
do_mating_events() (slim.simulation.cage.Cage method)
DOMINANT (slim.types.TreatmentTypes.HeterozygousResistance attribute)
dump_as_dataframe() (slim.simulation.simulator.Simulator static method)
dump_optimiser_as_pd() (slim.simulation.simulator.Simulator static method)
E
effectiveness_duration_days (slim.types.QueueTypes.TreatmentEvent attribute)
EggBatch (class in slim.types.QueueTypes)
Eggs (slim.gui_utils.model.CurveListState attribute)
EMB (class in slim.types.TreatmentTypes)
(slim.types.TreatmentTypes.Treatment attribute)
end_application_date (slim.types.QueueTypes.TreatmentEvent attribute)
enforceAspectRatio() (slim.gui_utils.plots.SmoothedGraphicsLayoutWidget method)
Event (class in slim.types.QueueTypes)
event_time (slim.types.QueueTypes.CageEvent property)
(slim.types.QueueTypes.DamAvailabilityBatch property)
(slim.types.QueueTypes.EggBatch property)
(slim.types.QueueTypes.TravellingEggBatch property)
(slim.types.QueueTypes.TreatmentEvent property)
execute_command() (slim.gui_utils.console.ConsoleWidget method)
exportPlots() (slim.gui_utils.plots.SingleRunPlotPane method)
ExtP (slim.gui_utils.model.CurveListState attribute)
F
failed (slim.SeaLiceMgmtGUI.OptimiserLoadingWorker attribute)
(slim.SeaLiceMgmtGUI.SimulatorLoadingWorker attribute)
fallow() (slim.simulation.cage.Cage method)
Farm (class in slim.simulation.farm)
FarmCommand (class in slim.types.QueueTypes)
FarmResponse (class in slim.types.QueueTypes)
finished (slim.SeaLiceMgmtGUI.OptimiserLoadingWorker attribute)
(slim.SeaLiceMgmtGUI.SimulatorLoadingWorker attribute)
first_application_date (slim.types.QueueTypes.TreatmentEvent attribute)
free_dams() (slim.simulation.lice_population.LicePopulation method)
from_ratios() (slim.simulation.lice_population.GenoDistrib static method)
G
generate_argparse_from_config() (slim.simulation.config.Config static method)
generate_eggs_discrete_batch() (slim.simulation.cage.Cage method)
generate_eggs_maternal_batch() (slim.simulation.cage.Cage static method)
generate_sampling_events() (slim.simulation.farm.Farm method)
generate_treatment_event() (slim.simulation.farm.Farm method)
GeneticMechanism (class in slim.types.TreatmentTypes)
geno_distrib (slim.types.QueueTypes.DamAvailabilityBatch attribute)
(slim.types.QueueTypes.EggBatch attribute)
(slim.types.QueueTypes.TravellingEggBatch attribute)
GenoDistrib (class in slim.simulation.lice_population)
GenoTreatmentValue (class in slim.simulation.lice_population)
get_allele_heterozygous_trait() (slim.types.TreatmentTypes.TreatmentParams static method)
get_arrivals() (slim.simulation.cage.Cage method)
get_background_lice_mortality() (slim.simulation.cage.Cage method)
get_cage_allocation() (slim.simulation.farm.Farm method)
get_cage_arrivals_stats() (slim.simulation.farm.Farm static method)
get_cage_pressures() (slim.simulation.farm.Farm method)
get_dying_lice_from_dead_fish() (slim.simulation.cage.Cage method)
get_egg_batch() (slim.simulation.cage.Cage method)
get_empty_geno_distrib() (slim.simulation.lice_population.LicePopulation static method)
get_external_pressure() (slim.simulation.simulator.Organisation method)
get_farm_allocation() (slim.simulation.farm.Farm method)
get_fish_growth() (slim.simulation.cage.Cage method)
get_fish_mortality_occurrences() (slim.types.TreatmentTypes.TreatmentParams method)
get_fish_treatment_mortality() (slim.simulation.cage.Cage method)
get_infecting_population() (slim.simulation.cage.Cage method)
get_infection_rates() (slim.simulation.cage.Cage method)
get_lice_lifestage() (slim.simulation.cage.Cage method)
get_lice_treatment_mortality() (slim.simulation.cage.Cage method)
get_lice_treatment_mortality_rate() (slim.simulation.cage.Cage method)
(slim.types.TreatmentTypes.EMB method)
(slim.types.TreatmentTypes.Thermolicer method)
(slim.types.TreatmentTypes.TreatmentParams method)
get_mean_infected_fish() (slim.simulation.cage.Cage method)
get_neighbour() (slim.Optimiser.Optimiser method)
get_num_eggs() (slim.simulation.cage.Cage method)
get_num_matings() (slim.simulation.cage.Cage method)
get_profit() (slim.simulation.farm.Farm method)
get_reservoir_lice() (slim.simulation.cage.Cage method)
get_simulation_path() (slim.simulation.simulator.Simulator static method)
get_simulator_from_probas() (slim.Optimiser.Optimiser method)
get_stage_ages_distrib() (slim.simulation.cage.Cage method)
get_temperature() (slim.simulation.cage.Cage method)
get_treatment() (slim.simulation.config.Config method)
get_variance_infected_fish() (slim.simulation.cage.Cage static method)
gross (slim.simulation.lice_population.GenoDistrib property)
H
handle_farm_messages() (slim.simulation.simulator.Organisation method)
hatch_date (slim.types.QueueTypes.EggBatch attribute)
(slim.types.QueueTypes.TravellingEggBatch attribute)
heightForWidth() (slim.gui_utils.plots.SmoothedPlotItemWrap method)
helpContent() (slim.SeaLiceMgmtGUI.Window method)
HeterozygousResistance (class in slim.types.TreatmentTypes)
I
INCOMPLETELY_DOMINANT (slim.types.TreatmentTypes.HeterozygousResistance attribute)
is_fallowing (slim.simulation.cage.Cage property)
is_positive() (slim.simulation.lice_population.GenoDistrib method)
is_treated() (slim.simulation.cage.Cage method)
iterations (slim.Optimiser.Optimiser attribute)
L
L1 (slim.gui_utils.model.CurveListState attribute)
L2 (slim.gui_utils.model.CurveListState attribute)
L3 (slim.gui_utils.model.CurveListState attribute)
L4 (slim.gui_utils.model.CurveListState attribute)
L5f (slim.gui_utils.model.CurveListState attribute)
L5m (slim.gui_utils.model.CurveListState attribute)
largest_remainder() (in module slim.simulation.lice_population)
lice_genomics (slim.simulation.farm.Farm property)
lice_population (slim.simulation.farm.Farm property)
lice_stages (slim.simulation.lice_population.LicePopulation attribute)
lice_stages_bio_labels (slim.simulation.lice_population.LicePopulation attribute)
lice_stages_bio_long_names (slim.simulation.lice_population.LicePopulation attribute)
LicePopulation (class in slim.simulation.lice_population)
LightModeMixin (class in slim.gui_utils.plots)
loadedOptimiserState (slim.SeaLiceMgmtGUI.Window attribute)
loadedSimulatorState (slim.SeaLiceMgmtGUI.Window attribute)
LocationTemps (class in slim.simulation.farm)
log() (slim.LoggableMixin method)
LoggableMixin (class in slim)
M
MATERNAL (slim.types.TreatmentTypes.GeneticMechanism attribute)
module
slim
slim.gui_utils
slim.gui_utils.configuration
slim.gui_utils.console
slim.gui_utils.model
slim.gui_utils.plots
slim.JSONEncoders
slim.Optimiser
slim.SeaLiceMgmt
slim.SeaLiceMgmtGUI
slim.simulation
slim.simulation.cage
slim.simulation.config
slim.simulation.farm
slim.simulation.lice_population
slim.simulation.simulator
slim.types
slim.types.QueueTypes
slim.types.TreatmentTypes
mortality_rate (slim.simulation.lice_population.GenoTreatmentValue attribute)
mutate() (slim.simulation.cage.Cage method)
N
name (slim.types.TreatmentTypes.EMB attribute)
(slim.types.TreatmentTypes.Thermolicer attribute)
(slim.types.TreatmentTypes.TreatmentParams attribute)
newAverageFactor (slim.gui_utils.plots.SmoothedGraphicsLayoutWidget attribute)
newConfig (slim.gui_utils.configuration.ConfigurationPane attribute)
newKernelSize (slim.gui_utils.plots.SmoothedGraphicsLayoutWidget attribute)
normalise_to() (slim.simulation.lice_population.GenoDistrib method)
northing (slim.simulation.farm.LocationTemps attribute)
num_fish (slim.simulation.farm.Farm property)
num_susc (slim.simulation.lice_population.GenoTreatmentValue attribute)
O
openOptimiserDump() (slim.SeaLiceMgmtGUI.Window method)
openSimulatorDump() (slim.SeaLiceMgmtGUI.Window method)
Optimiser (class in slim.Optimiser)
optimiser_seed (slim.Optimiser.Optimiser attribute)
OptimiserLoadingWorker (class in slim.SeaLiceMgmtGUI)
OptimiserPlotPane (class in slim.gui_utils.plots)
Organisation (class in slim.simulation.simulator)
P
paperMode (slim.gui_utils.plots.LightModeMixin property)
parse_pheno_resistance() (slim.types.TreatmentTypes.TreatmentParams static method)
pathogenic_stages (slim.simulation.lice_population.LicePopulation attribute)
plot() (slim.gui_utils.plots.SmoothedPlotItemWrap method)
pop_from_queue() (in module slim.types.QueueTypes)
print_text() (slim.gui_utils.console.ConsoleWidget method)
promote_population() (slim.simulation.cage.Cage method)
push_vars() (slim.gui_utils.console.ConsoleWidget method)
R
raw_update_value() (slim.simulation.lice_population.LicePopulation method)
recentFilesList (slim.SeaLiceMgmtGUI.Window property)
RECESSIVE (slim.types.TreatmentTypes.HeterozygousResistance attribute)
reload() (slim.simulation.simulator.Simulator static method)
reload_all_dump() (slim.simulation.simulator.Simulator static method)
reload_from_optimiser() (slim.simulation.simulator.Simulator static method)
remove_negatives() (slim.simulation.lice_population.LicePopulation method)
repeat_experiment (slim.Optimiser.Optimiser attribute)
request_date (slim.types.QueueTypes.FarmCommand attribute)
(slim.types.QueueTypes.SampleRequestCommand attribute)
response_date (slim.types.QueueTypes.FarmResponse attribute)
run() (slim.SeaLiceMgmtGUI.OptimiserLoadingWorker method)
(slim.SeaLiceMgmtGUI.SimulatorLoadingWorker method)
run_model() (slim.simulation.simulator.Simulator method)
S
SampleRequestCommand (class in slim.types.QueueTypes)
sampling_date (slim.types.QueueTypes.SamplingEvent attribute)
SamplingEvent (class in slim.types.QueueTypes)
SamplingResponse (class in slim.types.QueueTypes)
save() (slim.Optimiser.Optimiser method)
ScientificAxisItem (class in slim.gui_utils.plots)
select_lice() (slim.simulation.cage.Cage method)
set() (slim.simulation.lice_population.GenoDistrib method)
setAverageFactor() (slim.gui_utils.plots.SmoothedPlotItemWrap method)
setGenotype() (slim.gui_utils.plots.SingleRunPlotPane method)
setPaperMode() (slim.gui_utils.plots.LightModeMixin method)
setSmoothingFactor() (slim.gui_utils.plots.SmoothedPlotItemWrap method)
showGenotype (slim.gui_utils.plots.SingleRunPlotPane property)
sim_name (slim.gui_utils.model.SimulatorSingleRunState attribute)
Simulator (class in slim.simulation.simulator)
SimulatorLoadingWorker (class in slim.SeaLiceMgmtGUI)
SimulatorOptimiserState (class in slim.gui_utils.model)
SimulatorSingleRunState (class in slim.gui_utils.model)
SingleRunPlotPane (class in slim.gui_utils.plots)
slim
module
slim.gui_utils
module
slim.gui_utils.configuration
module
slim.gui_utils.console
module
slim.gui_utils.model
module
slim.gui_utils.plots
module
slim.JSONEncoders
module
slim.Optimiser
module
slim.SeaLiceMgmt
module
slim.SeaLiceMgmtGUI
module
slim.simulation
module
slim.simulation.cage
module
slim.simulation.config
module
slim.simulation.farm
module
slim.simulation.lice_population
module
slim.simulation.simulator
module
slim.types
module
slim.types.QueueTypes
module
slim.types.TreatmentTypes
module
SmoothedGraphicsLayoutWidget (class in slim.gui_utils.plots)
SmoothedPlotItemWrap (class in slim.gui_utils.plots)
starting_cfg (slim.Optimiser.Optimiser attribute)
states (slim.gui_utils.model.SimulatorOptimiserState attribute)
states_as_df (slim.gui_utils.model.SimulatorOptimiserState attribute)
(slim.gui_utils.model.SimulatorSingleRunState attribute)
step() (slim.simulation.simulator.Organisation method)
susceptible_stages (slim.simulation.lice_population.LicePopulation attribute)
T
temperatures (slim.simulation.farm.LocationTemps attribute)
ThermalTreatment (class in slim.types.TreatmentTypes)
Thermolicer (class in slim.types.TreatmentTypes)
THERMOLICER (slim.types.TreatmentTypes.Treatment attribute)
tickStrings() (slim.gui_utils.plots.ScientificAxisItem method)
times (slim.gui_utils.model.SimulatorSingleRunState attribute)
to_dt() (in module slim.simulation.config)
to_json() (slim.simulation.simulator.Organisation method)
to_json_dict() (slim.simulation.cage.Cage method)
(slim.simulation.farm.Farm method)
(slim.simulation.lice_population.GenoDistrib method)
(slim.simulation.lice_population.LicePopulation method)
(slim.simulation.simulator.Organisation method)
(slim.types.QueueTypes.Event method)
TravellingEggBatch (class in slim.types.QueueTypes)
Treatment (class in slim.types.TreatmentTypes)
treatment_type (slim.types.QueueTypes.TreatmentEvent attribute)
treatment_window (slim.types.QueueTypes.TreatmentEvent property)
TreatmentEvent (class in slim.types.QueueTypes)
TreatmentParams (class in slim.types.TreatmentTypes)
U
update() (slim.simulation.cage.Cage method)
(slim.simulation.farm.Farm method)
update_arrivals() (slim.simulation.cage.Cage method)
update_deltas() (slim.simulation.cage.Cage method)
update_genetic_ratios() (slim.simulation.simulator.Organisation method)
W
Window (class in slim.SeaLiceMgmtGUI)
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