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Quickstart
Outbreak Detection
User Guide
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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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Q
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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
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X
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Y
A
alpha (epysurv.models.timepoint.Bayes attribute)
(epysurv.models.timepoint.Boda attribute)
(epysurv.models.timepoint.CDC attribute)
(epysurv.models.timepoint.EarsC1 attribute)
(epysurv.models.timepoint.EarsC2 attribute)
(epysurv.models.timepoint.EarsC3 attribute)
(epysurv.models.timepoint.Farrington attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
(epysurv.models.timepoint.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.bayes.Bayes attribute)
(epysurv.models.timepoint.boda.Boda attribute)
(epysurv.models.timepoint.cdc.CDC attribute)
(epysurv.models.timepoint.ears.EarsC1 attribute)
(epysurv.models.timepoint.ears.EarsC2 attribute)
(epysurv.models.timepoint.ears.EarsC3 attribute)
(epysurv.models.timepoint.farrington.Farrington attribute)
(epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
(epysurv.models.timepoint.glr.GLRNegativeBinomial attribute)
B
baseline (epysurv.models.timepoint.ears.EarsC1 attribute)
(epysurv.models.timepoint.EarsC1 attribute)
(epysurv.models.timepoint.EarsC2 attribute)
(epysurv.models.timepoint.EarsC3 attribute)
(epysurv.models.timepoint.ears.EarsC2 attribute)
(epysurv.models.timepoint.ears.EarsC3 attribute)
Bayes (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.bayes)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
Boda (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.boda)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
C
CDC (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.cdc)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
change (epysurv.models.timepoint.glr.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRPoisson attribute)
,
[1]
(epysurv.models.timepoint.glr.GLRPoisson attribute)
,
[1]
county (epysurv.data.filter_combination.FilterCombination attribute)
Cusum (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.cusum)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
D
data (epysurv.data.filter_combination.FilterCombination attribute)
decision_boundary (epysurv.models.timepoint.Cusum attribute)
(epysurv.models.timepoint.cusum.Cusum attribute)
direction (epysurv.models.timepoint.glr.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRPoisson attribute)
,
[1]
(epysurv.models.timepoint.glr.GLRPoisson attribute)
,
[1]
disease (epysurv.data.filter_combination.FilterCombination attribute)
E
EarsC1 (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.ears)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
EarsC2 (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.ears)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
EarsC3 (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.ears)
epysurv (module)
epysurv.data (module)
epysurv.data.disease_loader (module)
epysurv.data.filter_combination (module)
epysurv.data.salmonella_data (module)
epysurv.data.utils (module)
epysurv.metrics (module)
epysurv.metrics.outbreak_detection (module)
epysurv.models (module)
epysurv.models.timepoint (module)
epysurv.models.timepoint.bayes (module)
epysurv.models.timepoint.boda (module)
epysurv.models.timepoint.cdc (module)
epysurv.models.timepoint.cusum (module)
epysurv.models.timepoint.ears (module)
epysurv.models.timepoint.farrington (module)
epysurv.models.timepoint.glr (module)
epysurv.models.timepoint.hmm (module)
epysurv.models.timepoint.outbreak_p (module)
epysurv.models.timepoint.rki (module)
epysurv.models.timeseries (module)
epysurv.models.timeseries.convert_interface (module)
epysurv.simulation (module)
epysurv.simulation.naive_poisson (module)
epysurv.visualization (module)
epysurv.visualization.model_diagnostics (module)
equal_covariate_effects (epysurv.models.timepoint.HMM attribute)
(epysurv.models.timepoint.hmm.HMM attribute)
expanding_windows() (epysurv.data.filter_combination.FilterCombination method)
expected_numbers_method (epysurv.models.timepoint.Cusum attribute)
(epysurv.models.timepoint.cusum.Cusum attribute)
F
Farrington (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.farrington)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
FarringtonFlexible (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.farrington)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
FilterCombination (class in epysurv.data.filter_combination)
from_ts_input() (epysurv.data.filter_combination.SplitYears class method)
G
get_outbreak_begins() (in module epysurv.simulation.naive_poisson)
ghozzi_case_score() (in module epysurv.metrics.outbreak_detection)
ghozzi_score() (in module epysurv.metrics)
(in module epysurv.metrics.outbreak_detection)
ghozzi_score_plot() (in module epysurv.visualization.model_diagnostics)
glr_test_threshold (epysurv.models.timepoint.glr.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRPoisson attribute)
,
[1]
(epysurv.models.timepoint.glr.GLRPoisson attribute)
,
[1]
GLRNegativeBinomial (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.glr)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
GLRPoisson (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.glr)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
H
HMM (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.hmm)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
I
include_recent_year (epysurv.models.timepoint.Bayes attribute)
(epysurv.models.timepoint.RKI attribute)
(epysurv.models.timepoint.bayes.Bayes attribute)
(epysurv.models.timepoint.rki.RKI attribute)
L
load_diseases() (in module epysurv.data)
(in module epysurv.data.disease_loader)
M
m (epysurv.models.timepoint.glr.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRPoisson attribute)
,
[1]
(epysurv.models.timepoint.glr.GLRPoisson attribute)
,
[1]
max_upperbound_cases (epysurv.models.timepoint.outbreak_p.OutbreakP attribute)
(epysurv.models.timepoint.OutbreakP attribute)
mc_munu (epysurv.models.timepoint.Boda attribute)
(epysurv.models.timepoint.boda.Boda attribute)
mc_y (epysurv.models.timepoint.Boda attribute)
(epysurv.models.timepoint.boda.Boda attribute)
min_cases_in_past_periods (epysurv.models.timepoint.Farrington attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
(epysurv.models.timepoint.farrington.Farrington attribute)
(epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
min_sigma (epysurv.models.timepoint.ears.EarsC1 attribute)
(epysurv.models.timepoint.EarsC1 attribute)
(epysurv.models.timepoint.EarsC2 attribute)
(epysurv.models.timepoint.ears.EarsC2 attribute)
N
n_harmonics (epysurv.models.timepoint.HMM attribute)
(epysurv.models.timepoint.hmm.HMM attribute)
n_hidden_states (epysurv.models.timepoint.HMM attribute)
(epysurv.models.timepoint.hmm.HMM attribute)
n_observations (epysurv.models.timepoint.HMM attribute)
(epysurv.models.timepoint.hmm.HMM attribute)
negbin_alpha (epysurv.models.timepoint.Cusum attribute)
(epysurv.models.timepoint.cusum.Cusum attribute)
O
OutbreakP (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.outbreak_p)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
P
past_period_cutoff (epysurv.models.timepoint.Farrington attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
(epysurv.models.timepoint.farrington.Farrington attribute)
(epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
past_weeks_not_included (epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
pathogen (epysurv.data.filter_combination.FilterCombination attribute)
plot_confusion_matrix() (in module epysurv.visualization.model_diagnostics)
plot_prediction() (in module epysurv.visualization.model_diagnostics)
PointSource (class in epysurv.simulation)
power_transform (epysurv.models.timepoint.Farrington attribute)
(epysurv.models.timepoint.farrington.Farrington attribute)
prior (epysurv.models.timepoint.Boda attribute)
(epysurv.models.timepoint.boda.Boda attribute)
Q
quantile_method (epysurv.models.timepoint.Boda attribute)
(epysurv.models.timepoint.boda.Boda attribute)
R
reference_value (epysurv.models.timepoint.Cusum attribute)
(epysurv.models.timepoint.cusum.Cusum attribute)
reweight (epysurv.models.timepoint.Farrington attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
(epysurv.models.timepoint.farrington.Farrington attribute)
(epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
RKI (class in epysurv.models.timepoint)
(class in epysurv.models.timepoint.rki)
(class in epysurv.models.timeseries)
(class in epysurv.models.timeseries.convert_interface)
S
salmonella() (in module epysurv.data)
(in module epysurv.data.salmonella_data)
sampling_method (epysurv.models.timepoint.Boda attribute)
(epysurv.models.timepoint.boda.Boda attribute)
season (epysurv.models.timepoint.Boda attribute)
(epysurv.models.timepoint.boda.Boda attribute)
SeasonalNoiseNegativeBinomial (class in epysurv.simulation)
SeasonalNoisePoisson (class in epysurv.simulation)
simulate() (epysurv.simulation.PointSource method)
(epysurv.simulation.SeasonalNoiseNegativeBinomial method)
(epysurv.simulation.SeasonalNoisePoisson method)
simulate_outbreaks() (in module epysurv.simulation.naive_poisson)
SplitYears (class in epysurv.data.filter_combination)
T
test() (epysurv.data.salmonella_data.TimeseriesClassificationData property)
(epysurv.data.TimeseriesClassificationData property)
test_final() (epysurv.data.filter_combination.TimeseriesClassificationData property)
test_gen() (epysurv.data.filter_combination.TimeseriesClassificationData property)
(epysurv.data.TimeseriesClassificationData property)
(epysurv.data.salmonella_data.TimeseriesClassificationData property)
threshold (epysurv.models.timepoint.outbreak_p.OutbreakP attribute)
(epysurv.models.timepoint.OutbreakP attribute)
threshold_method (epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
timedelta_weeks() (in module epysurv.data.utils)
timeseries_classifaction_generator() (in module epysurv.data)
(in module epysurv.data.salmonella_data)
timeseries_classifcation() (in module epysurv.data)
(in module epysurv.data.salmonella_data)
TimeseriesClassificationData (class in epysurv.data)
(class in epysurv.data.filter_combination)
(class in epysurv.data.salmonella_data)
train() (epysurv.data.salmonella_data.TimeseriesClassificationData property)
(epysurv.data.TimeseriesClassificationData property)
train_final() (epysurv.data.filter_combination.TimeseriesClassificationData property)
train_gen() (epysurv.data.filter_combination.TimeseriesClassificationData property)
(epysurv.data.TimeseriesClassificationData property)
(epysurv.data.salmonella_data.TimeseriesClassificationData property)
transform (epysurv.models.timepoint.Cusum attribute)
(epysurv.models.timepoint.cusum.Cusum attribute)
trend (epysurv.models.timepoint.Boda attribute)
(epysurv.models.timepoint.Farrington attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
(epysurv.models.timepoint.HMM attribute)
(epysurv.models.timepoint.boda.Boda attribute)
(epysurv.models.timepoint.farrington.Farrington attribute)
(epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
(epysurv.models.timepoint.hmm.HMM attribute)
trend_threshold (epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
U
upperbound_statistic (epysurv.models.timepoint.glr.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRPoisson attribute)
,
[1]
(epysurv.models.timepoint.OutbreakP attribute)
(epysurv.models.timepoint.glr.GLRPoisson attribute)
,
[1]
(epysurv.models.timepoint.outbreak_p.OutbreakP attribute)
W
weights_threshold (epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
window_half_width (epysurv.models.timepoint.Bayes attribute)
(epysurv.models.timepoint.CDC attribute)
(epysurv.models.timepoint.Farrington attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
(epysurv.models.timepoint.RKI attribute)
(epysurv.models.timepoint.bayes.Bayes attribute)
(epysurv.models.timepoint.cdc.CDC attribute)
(epysurv.models.timepoint.farrington.Farrington attribute)
(epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
(epysurv.models.timepoint.rki.RKI attribute)
X
x_max (epysurv.models.timepoint.glr.GLRNegativeBinomial attribute)
(epysurv.models.timepoint.GLRNegativeBinomial attribute)
Y
years_back (epysurv.models.timepoint.Bayes attribute)
(epysurv.models.timepoint.CDC attribute)
(epysurv.models.timepoint.Farrington attribute)
(epysurv.models.timepoint.FarringtonFlexible attribute)
(epysurv.models.timepoint.RKI attribute)
(epysurv.models.timepoint.bayes.Bayes attribute)
(epysurv.models.timepoint.cdc.CDC attribute)
(epysurv.models.timepoint.farrington.Farrington attribute)
(epysurv.models.timepoint.farrington.FarringtonFlexible attribute)
(epysurv.models.timepoint.rki.RKI attribute)
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