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JohannesPongeJohannesPonge
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Merge pull request #62 from IMMIDD/disease-model-update
Disease model update
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‎Project.toml‎

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
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name = "GEMS"
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uuid = "be47d99e-7859-414d-a902-bf4cb6b83c8a"
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version = "0.6.3"
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version = "0.7.0"
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authors = ["Johannes Ponge", "Janik Suer", "Lukas Bayer", "Wolfgang Bock", "Julian Patzner"]
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[deps]

‎data/DefaultConf.toml‎

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Original file line numberDiff line numberDiff line change
@@ -3,16 +3,18 @@
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# seed = 1234
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tickunit = 'd'
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GlobalSetting = false
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startdate = '2024.01.01'
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enddate = '2024.12.31'
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startdate = '2024-01-01'
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enddate = '2024-12-31'
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[Simulation.StartCondition]
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type = "InfectedFraction"
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fraction = 0.001
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pathogen = "Covid19" # BE AWARE, THAT NAME MUST BE THE SAME AS IN TOML SECTION
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[Simulation.StartCondition.parameters]
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fraction = 0.001
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#pathogen = "Covid19"
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[Simulation.StopCriterion]
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type = "TimesUp"
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limit = 365
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[Simulation.StopCriterion.parameters]
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limit = 365
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[Population]
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n = 100_000
@@ -29,64 +31,147 @@
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[Pathogens.Covid19.transmission_function.parameters]
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transmission_rate = 0.2
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[Pathogens.Covid19.onset_of_symptoms]
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distribution = "Poisson"
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parameters = [3]
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[Pathogens.Covid19.time_to_recovery]
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distribution = "Poisson"
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parameters = [7]
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[Pathogens.Covid19.onset_of_severeness]
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distribution = "Poisson"
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parameters = [3]
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[Pathogens.Covid19.infectious_offset]
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distribution = "Poisson"
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parameters = [1]
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[Pathogens.Covid19.mild_death_rate]
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distribution = "Binomial"
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parameters = [1, 0.0]
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[Pathogens.Covid19.severe_death_rate]
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distribution = "Binomial"
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parameters = [1, 0.05]
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[Pathogens.Covid19.critical_death_rate]
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distribution = "Binomial"
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parameters = [1, 0.2]
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[Pathogens.Covid19.hospitalization_rate]
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distribution = "Binomial"
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parameters = [1, 0.3]
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[Pathogens.Covid19.ventilation_rate]
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distribution = "Binomial"
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parameters = [1, 0.3]
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[Pathogens.Covid19.icu_rate]
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distribution = "Binomial"
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parameters = [1, 0.3]
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[Pathogens.Covid19.time_to_hospitalization]
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distribution = "Poisson"
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parameters = [7]
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[Pathogens.Covid19.time_to_icu]
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distribution = "Poisson"
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parameters = [7]
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[Pathogens.Covid19.length_of_stay]
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distribution = "Poisson"
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parameters = [7]
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[Pathogens.Covid19.dpr]
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# Matrix with Disease Progression
87-
age_groups = ["0+"]
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disease_compartments = ["Asymptomatic", "Mild", "Severe", "Critical"]
89-
stratification_matrix = [[0.4, 0.45, 0.1, 0.05]]
34+
[Pathogens.Covid19.progressions]
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36+
# ASYMPTOMATIC PROGRESSION [TOTAL DURATION ~ 10 DAYS]
37+
[Pathogens.Covid19.progressions.Asymptomatic]
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# time to infectiousness (after exposure) [+1 will be added internally to avoid zero-day durations]
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[Pathogens.Covid19.progressions.Asymptomatic.exposure_to_infectiousness_onset]
40+
distribution = "Poisson"
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parameters = [1]
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# time to recovery (after infectiousness onset)
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[Pathogens.Covid19.progressions.Asymptomatic.infectiousness_onset_to_recovery]
44+
distribution = "Poisson"
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parameters = [8]
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47+
# SYMPTOMATIC PROGRESSION [TOTAL DURATION ~ 10 DAYS]
48+
[Pathogens.Covid19.progressions.Symptomatic]
49+
# time to infectiousness (after exposure) [+1 will be added internally to avoid zero-day durations]
50+
[Pathogens.Covid19.progressions.Symptomatic.exposure_to_infectiousness_onset]
51+
distribution = "Poisson"
52+
parameters = [1]
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# time to symptom onset (after infectiousness onset)
54+
[Pathogens.Covid19.progressions.Symptomatic.infectiousness_onset_to_symptom_onset]
55+
distribution = "Poisson"
56+
parameters = [1]
57+
# time to recovery (after symptom onset)
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[Pathogens.Covid19.progressions.Symptomatic.symptom_onset_to_recovery]
59+
distribution = "Poisson"
60+
parameters = [7]
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62+
# SEVERE PROGRESSION [TOTAL DURATION ~ 15 DAYS]
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[Pathogens.Covid19.progressions.Severe]
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# time to infectiousness (after exposure) [+1 will be added internally to avoid zero-day durations]
65+
[Pathogens.Covid19.progressions.Severe.exposure_to_infectiousness_onset]
66+
distribution = "Poisson"
67+
parameters = [1]
68+
# time to symptom onset (after infectiousness onset)
69+
[Pathogens.Covid19.progressions.Severe.infectiousness_onset_to_symptom_onset]
70+
distribution = "Poisson"
71+
parameters = [1]
72+
# time to severeness onset (after symptom onset)
73+
[Pathogens.Covid19.progressions.Severe.symptom_onset_to_severeness_onset]
74+
distribution = "Poisson"
75+
parameters = [1]
76+
# time to severeness offset (after severeness onset)
77+
[Pathogens.Covid19.progressions.Severe.severeness_onset_to_severeness_offset]
78+
distribution = "Poisson"
79+
parameters = [7]
80+
# time to recovery (after severeness offset)
81+
[Pathogens.Covid19.progressions.Severe.severeness_offset_to_recovery]
82+
distribution = "Poisson"
83+
parameters = [4]
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85+
# HOSPITALIZED PROGRESSION [TOTAL DURATION ~ 20 DAYS]
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[Pathogens.Covid19.progressions.Hospitalized]
87+
# time to infectiousness (after exposure) [+1 will be added internally to avoid zero-day durations]
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[Pathogens.Covid19.progressions.Hospitalized.exposure_to_infectiousness_onset]
89+
distribution = "Poisson"
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parameters = [1]
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# time to symptom onset (after infectiousness onset)
92+
[Pathogens.Covid19.progressions.Hospitalized.infectiousness_onset_to_symptom_onset]
93+
distribution = "Poisson"
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parameters = [1]
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# time to severeness onset (after symptom onset)
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[Pathogens.Covid19.progressions.Hospitalized.symptom_onset_to_severeness_onset]
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distribution = "Poisson"
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parameters = [1]
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# time to hospitalization (after severeness onset)
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[Pathogens.Covid19.progressions.Hospitalized.severeness_onset_to_hospital_admission]
101+
distribution = "Poisson"
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parameters = [2]
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# time to recovery (after hospitalization)
104+
[Pathogens.Covid19.progressions.Hospitalized.hospital_admission_to_hospital_discharge]
105+
distribution = "Poisson"
106+
parameters = [7]
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# time to recovery (after hospital discharge)
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[Pathogens.Covid19.progressions.Hospitalized.hospital_discharge_to_severeness_offset]
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distribution = "Poisson"
110+
parameters = [3]
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[Pathogens.Covid19.progressions.Hospitalized.severeness_offset_to_recovery]
112+
distribution = "Poisson"
113+
parameters = [4]
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115+
# CRITICAL PROGRESSION [TOTAL DURATION ~ 30 DAYS]
116+
[Pathogens.Covid19.progressions.Critical]
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# probability of death (after ICU admission)
118+
death_probability = 0.3
119+
120+
# time to infectiousness (after exposure) [+1 will be added internally to avoid zero-day durations]
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[Pathogens.Covid19.progressions.Critical.exposure_to_infectiousness_onset]
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distribution = "Poisson"
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parameters = [1]
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# time to symptom onset (after infectiousness onset)
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[Pathogens.Covid19.progressions.Critical.infectiousness_onset_to_symptom_onset]
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distribution = "Poisson"
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parameters = [1]
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# time to severeness onset (after symptom onset)
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[Pathogens.Covid19.progressions.Critical.symptom_onset_to_severeness_onset]
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distribution = "Poisson"
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parameters = [1]
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# time to hospitalization (after severeness onset)
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[Pathogens.Covid19.progressions.Critical.severeness_onset_to_hospital_admission]
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distribution = "Poisson"
135+
parameters = [2]
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# time to ICU admission (after hospitalization)
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[Pathogens.Covid19.progressions.Critical.hospital_admission_to_icu_admission]
138+
distribution = "Poisson"
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parameters = [2]
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141+
# RECOVERY PATHWAY
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# time to ICU discharge (after ICU admission)
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[Pathogens.Covid19.progressions.Critical.icu_admission_to_icu_discharge]
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distribution = "Poisson"
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parameters = [7]
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# time to hospital discharge (after ICU discharge)
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[Pathogens.Covid19.progressions.Critical.icu_discharge_to_hospital_discharge]
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distribution = "Poisson"
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parameters = [7]
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# time to recovery (after hospital discharge)
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[Pathogens.Covid19.progressions.Critical.hospital_discharge_to_severeness_offset]
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distribution = "Poisson"
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parameters = [3]
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[Pathogens.Covid19.progressions.Critical.severeness_offset_to_recovery]
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distribution = "Poisson"
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parameters = [4]
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# DEATH PATHWAY
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# time to death (after ICU admission)
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[Pathogens.Covid19.progressions.Critical.icu_admission_to_death]
161+
distribution = "Poisson"
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parameters = [10]
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164+
# progression assignment method
165+
[Pathogens.Covid19.progression_assignment]
166+
type = "AgeBasedProgressionAssignment"
167+
[Pathogens.Covid19.progression_assignment.parameters]
168+
#progression_categories = ["Asymptomatic", "Symptomatic", "Hospitalized", "Critical"]
169+
# Matrix with Disease Progression
170+
age_groups = ["-14", "15-65", "66-"]
171+
progression_categories = ["Asymptomatic", "Symptomatic", "Severe", "Hospitalized", "Critical"]
172+
stratification_matrix = [[0.400, 0.580, 0.010, 0.007, 0.003], # age group -14
173+
[0.250, 0.600, 0.110, 0.030, 0.010], # age group 15-65
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[0.150, 0.400, 0.250, 0.120, 0.080]] # age group 66-
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[Settings]
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‎docs/make.jl‎

Lines changed: 6 additions & 5 deletions
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@@ -34,11 +34,12 @@ makedocs(
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"1 - Getting Started" => "tut_gettingstarted.md",
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"2 - Exploring Models" => "tut_exploring.md",
3636
"3 - Plotting" =>"tut_plotting.md",
37-
"4 - Running Batches" => "tut_batches.md",
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"5 - Creating Populations" => "tut_pops.md",
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"6 - Advanced Parameterization" => "tut_configfiles.md",
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"7 - Logging & Post-Processing" => "tut_postprocessing.md",
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"8 - Reporting" => "tut_reporting.md",
37+
"4 - Configuring Diseases" =>"tut_diseases.md",
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"5 - Running Batches" => "tut_batches.md",
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"6 - Creating Populations" => "tut_pops.md",
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"7 - Advanced Parameterization" => "tut_configfiles.md",
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"8 - Logging & Post-Processing" => "tut_postprocessing.md",
42+
#"8 - Reporting" => "tut_reporting.md",
4243
"9 - Modeling Interventions" =>"tut_npi.md",
4344
#"10 - Modeling Behavior" =>"tut_behavior.md",
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#"11 - Contact Structures" =>"tut_contacts.md",

‎docs/src/api_batch.md‎

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### Constructors
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1818
```@docs
19-
Batch(;::Integer::Bool, simargs...)
20-
Batch(::Simulation...)
21-
Batch(::Vector{Simulation})
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Batch(::Batch...)
23-
Batch(::Vector{Batch})
19+
Batch
2420
```
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2622
### Functions
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3935
## BatchProcessor
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41-
### SConstructors
37+
### Constructors
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4339
```@docs
44-
BatchProcessor(::Vector{ResultData})
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BatchProcessor(::Batch; ::Bool)
40+
BatchProcessor
4641
```
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### Functions
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5449
cumulative_disease_progressions(::BatchProcessor)
5550
cumulative_quarantines(::BatchProcessor)
5651
effectiveR(::BatchProcessor)
52+
extract
53+
extract_unique
5754
number_of_individuals(::BatchProcessor)
5855
pathogens(::BatchProcessor)
59-
pathogens_by_name(::BatchProcessor)
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population_files(::BatchProcessor)
6157
population_pyramid(::BatchProcessor)
6258
run_ids(::BatchProcessor)
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8278
### Constructors
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8480
```@docs
85-
BatchData(::BatchProcessor; ::String)
86-
BatchData(::Batch; ::String, ::String)
87-
BatchData(::Vector{ResultData}; ::String)
88-
BatchData(::BatchData...; ::String)
89-
BatchData(::Vector{BatchData}; ::String)
81+
BatchData
9082
```
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### Functions

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