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* Adjust parameters for testing specificity, dropout and compliance rates, fraction asymptomatic, mild fraction, and generation time distribution; adjust script for processing parameter dictionary so that whitespace is stripped from the parameter-type column before unique values are found
* Lower min number of cases to test in test_recursive_testing
Fix test_quarantine_household_on_symptoms to only look at index cases
from the end time. This is required because when we filter out
hospitalised people we only do it for the final time. Also remove
days_since_index/contact calcs which are no longer used.
* Fix hospital test test_interaction_type_representative
Missing ICU interactions due to the insufficient overall cases at the
end of the interaction. Increase the number of seed infections and
reduce the end_time to ensure a large number of cases and the end of the
test (hence ICU interactions).
Co-authored-by: roberthinch <[email protected]>
Copy file name to clipboardexpand all lines: documentation/parameters/active_intervention_parameters.md
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|`quarantine_length_traced_symptoms`| 14 | - | Maximum number of days quarantine for individuals who are traced after a contact reported symptoms | - |
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|`quarantine_length_traced_positive`| 14 | - | Maximum number of days quarantine for individuals who are traced after a contact tested positive | - |
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|`quarantine_length_positive`| 14 | - | Maximum number of days quarantine for individuals with a positive test result | - |
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|`quarantine_dropout_traced_symptoms`| 0.03| - | Daily probability of drop out for an individual quarantining after being traced following contact with an individual self-reporting symptoms | - |
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|`quarantine_dropout_traced_symptoms`| 0.04| - | Daily probability of drop out for an individual quarantining after being traced following contact with an individual self-reporting symptoms | - |
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|`quarantine_dropout_traced_positive`| 0.03 | - | Daily probability of drop out for an individual quarantining after being traced following contact with an individual who tested positive | - |
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|`quarantine_dropout_positive`| 0.02| - | Daily probability of drop out for an individual quarantining after a positive test result | - |
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|`quarantine_compliance_traced_symptoms`| 0.8| - | Fraction of individuals who initially comply with a quarantine notification after their contact reported symptoms | - |
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|`quarantine_dropout_positive`| 0.01| - | Daily probability of drop out for an individual quarantining after a positive test result | - |
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|`quarantine_compliance_traced_symptoms`| 0.5| - | Fraction of individuals who initially comply with a quarantine notification after their contact reported symptoms | - |
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|`quarantine_compliance_traced_positive`| 0.9 | - | Fraction of individuals who initially comply with a quarantine notification after their contact tested positive | - |
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|`test_on_symptoms`| 0 | - | Test individuals who show symptoms (0=no, 1=yes) | - |
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|`test_on_traced`| 0 | - | Test individuals who have been contact-traced (0=no, 1=yes) | - |
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|`test_release_on_negative`| 1 | - | Release individuals following a negative test (0=no, 1=yes) | - |
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|`trace_on_symptoms`| 0 | - | Trace contacts of individuals who show symptoms (0=no, 1=yes) | - |
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|`trace_on_positive`| 0 | - | Trace contacts of an individual who tests positive (0=no, 1=yes) | - |
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|`retrace_on_positive`| 0 | - | Repeat contract tracing be carried out on a positive test if already tested on symptoms (0=no, 1=yes) | - |
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|`retrace_on_positive`| 0 | - | Repeat contract tracing be carried out on a positive test if already traced on symptoms (0=no, 1=yes) | - |
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|`quarantine_on_traced`| 0 | - | Quarantine individuals who are traced (0=no, 1=yes) | - |
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|`traceable_interaction_fraction`| 0.8 | - | Fraction of interactions that are captured if both users have the app | - |
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|`tracing_network_depth`| 0 | - | Depth of interaction network to contact | - |
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|`quarantine_days`| 7 | - | The number of previous days' contacts to be traced and contacted | - |
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|`quarantine_smart_release_day`| 0 | - | Release a chain of quarantined people if after this number of days nobody has shown symptoms on the chain | - |
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|`test_insensitive_period`| 3 | - | Number of days following infection the test is insensitive | Woelfel et al. 2020 |
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|`test_sensitive_period`| 14 | - | Number of days following infection to end of period where test is sensitive | - |
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|`test_sensitivity`| 0.8 | - | Sensitivity of test in the time where it is sensitive | - |
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|`test_specificity`| 0.999 | - | Specificity of test (at any time) | - |
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|`test_order_wait`| 1 | - | Minimum number of days to wait to take a test | - |
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|`test_result_wait`| 1 | - | Number of days to wait for a test result | - |
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|`app_users_fraction_0_9`| 0.09 | - | Maximum fraction of the population with smartphones aged 0-9 | OFCOM 3-5 year olds |
Copy file name to clipboardexpand all lines: documentation/parameters/disease_dynamics_parameters.md
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|`sd_time_to_recover`| 5 |σ<sub>rec</sub> | Standard deviation of time to recovery if hospitalisaion is not required (days) | Yang et al 2020 |
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|`mean_time_to_death`| 11.74 |μ<sub>death</sub> | Mean time to death after acquiring critical care (days) | Personal communication with SPI-M; data soon to be published |
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|`sd_time_to_death`| 8.79 |σ<sub>death</sub> | Standard deviation of time to death after acquiring critical care (days) | Personal communication with SPI-M; data soon to be published |
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|`fraction_asymptomatic_0_9`| 0.16|φ<sub>asym</sub>(0-9) | Fraction of infected individuals who are asymptomatic, aged 0-9 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_10_19`| 0.16|φ<sub>asym</sub>(10-19) | Fraction of infected individuals who are asymptomatic, aged 10-19 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_20_29`| 0.16|φ<sub>asym</sub>(20-29) | Fraction of infected individuals who are asymptomatic, aged 20-29 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_30_39`| 0.16|φ<sub>asym</sub>(30-39) | Fraction of infected individuals who are asymptomatic, aged 30-39 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_40_49`| 0.16|φ<sub>asym</sub>(40-49) | Fraction of infected individuals who are asymptomatic, aged 40-49 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_50_59`| 0.16|φ<sub>asym</sub>(50-59) | Fraction of infected individuals who are asymptomatic, aged 50-59 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_60_69`| 0.16|φ<sub>asym</sub>(60-69) | Fraction of infected individuals who are asymptomatic, aged 60-69 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_70_79`| 0.16|φ<sub>asym</sub>(70-79) | Fraction of infected individuals who are asymptomatic, aged 70-79 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_80`| 0.16|φ<sub>asym</sub>(80) | Fraction of infected individuals who are asymptomatic, aged 80+ |Byambasuren et al. 2020|
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|`mild_fraction_0_9`| 0.79|φ<sub>mild</sub>(0-9) | Fraction of infected individuals with mild symptoms, aged 0-9 |de Souza et al. 2020 |
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|`mild_fraction_10_19`| 0.79|φ<sub>mild</sub>(10-19) | Fraction of infected individuals with mild symptoms, aged 10-19 |de Souza et al. 2020 |
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|`mild_fraction_20_29`| 0.73|φ<sub>mild</sub>(20-29) | Fraction of infected individuals with mild symptoms, aged 20-29 |Yang, Lu et al. 2020 |
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|`mild_fraction_30_39`| 0.68|φ<sub>mild</sub>(30-39) | Fraction of infected individuals with mild symptoms, aged 30-39 |Yang, Lu et al. 2020 |
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|`mild_fraction_40_49`| 0.65|φ<sub>mild</sub>(40-49) | Fraction of infected individuals with mild symptoms, aged 40-49 |Yang, Lu et al. 2020 |
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|`mild_fraction_50_59`| 0.59|φ<sub>mild</sub>(50-59) | Fraction of infected individuals with mild symptoms, aged 50-59 |Yang, Lu et al. 2020 |
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|`mild_fraction_60_69`| 0.53|φ<sub>mild</sub>(60-69) | Fraction of infected individuals with mild symptoms, aged 60-69 |Yang, Lu et al. 2020 |
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|`mild_fraction_70_79`| 0.41|φ<sub>mild</sub>(70-79) | Fraction of infected individuals with mild symptoms, aged 70-79 |Yang, Lu et al. 2020 |
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|`mild_fraction_80`| 0.27|φ<sub>mild</sub>(80) | Fraction of infected individuals with mild symptoms, aged 80+ |Yang, Lu et al. 2020 |
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|`fraction_asymptomatic_0_9`| 0.339|φ<sub>asym</sub>(0-9) | Fraction of infected individuals who are asymptomatic, aged 0-9 |-|
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|`fraction_asymptomatic_10_19`| 0.305|φ<sub>asym</sub>(10-19) | Fraction of infected individuals who are asymptomatic, aged 10-19 |-|
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|`fraction_asymptomatic_20_29`| 0.271|φ<sub>asym</sub>(20-29) | Fraction of infected individuals who are asymptomatic, aged 20-29 |-|
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|`fraction_asymptomatic_30_39`| 0.237|φ<sub>asym</sub>(30-39) | Fraction of infected individuals who are asymptomatic, aged 30-39 |-|
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|`fraction_asymptomatic_40_49`| 0.203|φ<sub>asym</sub>(40-49) | Fraction of infected individuals who are asymptomatic, aged 40-49 |-|
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|`fraction_asymptomatic_50_59`| 0.169|φ<sub>asym</sub>(50-59) | Fraction of infected individuals who are asymptomatic, aged 50-59 |-|
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|`fraction_asymptomatic_60_69`| 0.135|φ<sub>asym</sub>(60-69) | Fraction of infected individuals who are asymptomatic, aged 60-69 |-|
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|`fraction_asymptomatic_70_79`| 0.101|φ<sub>asym</sub>(70-79) | Fraction of infected individuals who are asymptomatic, aged 70-79 |-|
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|`fraction_asymptomatic_80`| 0.0667|φ<sub>asym</sub>(80) | Fraction of infected individuals who are asymptomatic, aged 80+ |-|
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|`mild_fraction_0_9`| 0.224|φ<sub>mild</sub>(0-9) | Fraction of infected individuals with mild symptoms, aged 0-9 |Riccardo et al. 2020 |
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|`mild_fraction_10_19`| 0.212|φ<sub>mild</sub>(10-19) | Fraction of infected individuals with mild symptoms, aged 10-19 |Riccardo et al. 2020 |
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|`mild_fraction_20_29`| 0.198|φ<sub>mild</sub>(20-29) | Fraction of infected individuals with mild symptoms, aged 20-29 |Riccardo et al. 2020 |
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|`mild_fraction_30_39`| 0.181|φ<sub>mild</sub>(30-39) | Fraction of infected individuals with mild symptoms, aged 30-39 |Riccardo et al. 2020 |
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|`mild_fraction_40_49`| 0.162|φ<sub>mild</sub>(40-49) | Fraction of infected individuals with mild symptoms, aged 40-49 |Riccardo et al. 2020 |
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|`mild_fraction_50_59`| 0.140|φ<sub>mild</sub>(50-59) | Fraction of infected individuals with mild symptoms, aged 50-59 |Riccardo et al. 2020 |
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|`mild_fraction_60_69`| 0.117|φ<sub>mild</sub>(60-69) | Fraction of infected individuals with mild symptoms, aged 60-69 |Riccardo et al. 2020 |
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|`mild_fraction_70_79`| 0.0906|φ<sub>mild</sub>(70-79) | Fraction of infected individuals with mild symptoms, aged 70-79 |Riccardo et al. 2020 |
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|`mild_fraction_80`| 0.0623|φ<sub>mild</sub>(80) | Fraction of infected individuals with mild symptoms, aged 80+ |Riccardo et al. 2020 |
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|`mean_asymptomatic_to_recovery`| 15 |μ<sub>a,rec</sub> | Mean time from infection to recovery (and no longer infectious) for an asymptomatic individual (days) | Yang et al 2020 |
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|`sd_asymptomatic_to_recovery`| 5 |σ<sub>a,rec</sub> | Standard deviation from infection to recovery for an asymptomatic individual (days) | Yang et al 2020 |
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|`hospitalised_fraction_0_9`| 0.01 |φ<sub>hosp</sub>(0-9) | Fraction of infected individuals with severe symptoms aged 0-9 who are hospitalised | Ferguson et al, 2020 |
Copy file name to clipboardexpand all lines: documentation/parameters/infection_parameters.md
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| Name | Value | Symbol | Description | Source |
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| ---- | ---- | ---- | ---- | ---- |
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|`n_seed_infection`| 5 | - | Number of infections seeded at simulation start | - |
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|`mean_infectious_period`|6|μ| Mean of the generation time distribution (days) |Ma et al, 2020; Ganyani et al. 2020; Ferretti & Wymant et al. 2022|
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|`sd_infectious_period`| 2.5|σ| Standard deviation (days) of infectious period |Ma et al, 2020; Ganyani et al. 2020; Ferretti & Wymant et al. 2022|
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|`mean_infectious_period`|5.5|μ| Mean of the generation time distribution (days) |Ferretti et al in prep 2020; Ferretti & Wymant et al 2020; Xia et al 2020; He et al 2020; Cheng et al 2020|
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|`sd_infectious_period`| 2.14|σ| Standard deviation (days) of infectious period |Ferretti et al in prep 2020; Ferretti & Wymant et al 2020; Xia et al 2020; He et al 2020; Cheng et al 2020|
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|`infectious_rate`| 5.64 |*R*| Mean number of individuals infected by each infectious individual with moderate to severe symptoms | Derived from calibration |
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|`asymptomatic_infectious_factor`| 0.29 |*A<sub>asym</sub>*| Infectious rate of asymptomatic individuals relative to symptomatic individuals | Luo et al 2020 |
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|`mild_infectious_factor`| 0.48 |*A<sub>mild</sub>*| Infectious rate of mildly symptomatic individuals relative to symptomatic individuals | Luo et al 2020 |
|`end_time`| 200 | - | End time (total number of simulated days) | - |
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|`n_seed_infection`| 5 | - | Number of infections seeded at simulation start | - |
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|`mean_infectious_period`|6|μ| Mean of the generation time distribution (days) |Ma et al, 2020; Ganyani et al. 2020; Ferretti & Wymant et al. 2022|
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|`sd_infectious_period`| 2.5|σ| Standard deviation (days) of infectious period |Ma et al, 2020; Ganyani et al. 2020; Ferretti & Wymant et al. 2022|
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|`mean_infectious_period`|5.5|μ| Mean of the generation time distribution (days) |Ferretti et al in prep 2020; Ferretti & Wymant et al 2020; Xia et al 2020; He et al 2020; Cheng et al 2020|
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|`sd_infectious_period`| 2.14|σ| Standard deviation (days) of infectious period |Ferretti et al in prep 2020; Ferretti & Wymant et al 2020; Xia et al 2020; He et al 2020; Cheng et al 2020|
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|`infectious_rate`| 5.64 |*R*| Mean number of individuals infected by each infectious individual with moderate to severe symptoms | Derived from calibration |
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|`mean_time_to_symptoms`| 5.42 |μ<sub>sym</sub> | Mean time from infection to onset of symptoms (days) | McAloon et al. |
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|`sd_time_to_symptoms`| 2.7 |σ<sub>sym</sub> | Standard deviation of time from infection to onset of symptoms (days) | McAloon et al. |
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|`sd_time_to_recover`| 5 |σ<sub>rec</sub> | Standard deviation of time to recovery if hospitalisaion is not required (days) | Yang et al 2020 |
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|`mean_time_to_death`| 11.74 |μ<sub>death</sub> | Mean time to death after acquiring critical care (days) | Personal communication with SPI-M; data soon to be published |
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|`sd_time_to_death`| 8.79 |σ<sub>death</sub> | Standard deviation of time to death after acquiring critical care (days) | Personal communication with SPI-M; data soon to be published |
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|`fraction_asymptomatic_0_9`| 0.16|φ<sub>asym</sub>(0-9) | Fraction of infected individuals who are asymptomatic, aged 0-9 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_10_19`| 0.16|φ<sub>asym</sub>(10-19) | Fraction of infected individuals who are asymptomatic, aged 10-19 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_20_29`| 0.16|φ<sub>asym</sub>(20-29) | Fraction of infected individuals who are asymptomatic, aged 20-29 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_30_39`| 0.16|φ<sub>asym</sub>(30-39) | Fraction of infected individuals who are asymptomatic, aged 30-39 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_40_49`| 0.16|φ<sub>asym</sub>(40-49) | Fraction of infected individuals who are asymptomatic, aged 40-49 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_50_59`| 0.16|φ<sub>asym</sub>(50-59) | Fraction of infected individuals who are asymptomatic, aged 50-59 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_60_69`| 0.16|φ<sub>asym</sub>(60-69) | Fraction of infected individuals who are asymptomatic, aged 60-69 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_70_79`| 0.16|φ<sub>asym</sub>(70-79) | Fraction of infected individuals who are asymptomatic, aged 70-79 |Byambasuren et al. 2020|
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|`fraction_asymptomatic_80`| 0.16|φ<sub>asym</sub>(80) | Fraction of infected individuals who are asymptomatic, aged 80+ |Byambasuren et al. 2020|
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|`fraction_asymptomatic_0_9`| 0.339|φ<sub>asym</sub>(0-9) | Fraction of infected individuals who are asymptomatic, aged 0-9 |-|
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|`fraction_asymptomatic_10_19`| 0.305|φ<sub>asym</sub>(10-19) | Fraction of infected individuals who are asymptomatic, aged 10-19 |-|
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|`fraction_asymptomatic_20_29`| 0.271|φ<sub>asym</sub>(20-29) | Fraction of infected individuals who are asymptomatic, aged 20-29 |-|
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|`fraction_asymptomatic_30_39`| 0.237|φ<sub>asym</sub>(30-39) | Fraction of infected individuals who are asymptomatic, aged 30-39 |-|
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|`fraction_asymptomatic_40_49`| 0.203|φ<sub>asym</sub>(40-49) | Fraction of infected individuals who are asymptomatic, aged 40-49 |-|
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|`fraction_asymptomatic_50_59`| 0.169|φ<sub>asym</sub>(50-59) | Fraction of infected individuals who are asymptomatic, aged 50-59 |-|
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|`fraction_asymptomatic_60_69`| 0.135|φ<sub>asym</sub>(60-69) | Fraction of infected individuals who are asymptomatic, aged 60-69 |-|
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|`fraction_asymptomatic_70_79`| 0.101|φ<sub>asym</sub>(70-79) | Fraction of infected individuals who are asymptomatic, aged 70-79 |-|
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|`fraction_asymptomatic_80`| 0.0667|φ<sub>asym</sub>(80) | Fraction of infected individuals who are asymptomatic, aged 80+ |-|
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|`asymptomatic_infectious_factor`| 0.29 |*A<sub>asym</sub>*| Infectious rate of asymptomatic individuals relative to symptomatic individuals | Luo et al 2020 |
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|`mild_fraction_0_9`| 0.79|φ<sub>mild</sub>(0-9) | Fraction of infected individuals with mild symptoms, aged 0-9 |de Souza et al. 2020 |
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|`mild_fraction_10_19`| 0.79|φ<sub>mild</sub>(10-19) | Fraction of infected individuals with mild symptoms, aged 10-19 |de Souza et al. 2020 |
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|`mild_fraction_20_29`| 0.73|φ<sub>mild</sub>(20-29) | Fraction of infected individuals with mild symptoms, aged 20-29 |Yang, Lu et al. 2020 |
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|`mild_fraction_30_39`| 0.68|φ<sub>mild</sub>(30-39) | Fraction of infected individuals with mild symptoms, aged 30-39 |Yang, Lu et al. 2020 |
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|`mild_fraction_40_49`| 0.65|φ<sub>mild</sub>(40-49) | Fraction of infected individuals with mild symptoms, aged 40-49 |Yang, Lu et al. 2020 |
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|`mild_fraction_50_59`| 0.59|φ<sub>mild</sub>(50-59) | Fraction of infected individuals with mild symptoms, aged 50-59 |Yang, Lu et al. 2020 |
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|`mild_fraction_60_69`| 0.53|φ<sub>mild</sub>(60-69) | Fraction of infected individuals with mild symptoms, aged 60-69 |Yang, Lu et al. 2020 |
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|`mild_fraction_70_79`| 0.41|φ<sub>mild</sub>(70-79) | Fraction of infected individuals with mild symptoms, aged 70-79 |Yang, Lu et al. 2020 |
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|`mild_fraction_80`| 0.27|φ<sub>mild</sub>(80) | Fraction of infected individuals with mild symptoms, aged 80+ |Yang, Lu et al. 2020 |
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|`mild_fraction_0_9`| 0.224|φ<sub>mild</sub>(0-9) | Fraction of infected individuals with mild symptoms, aged 0-9 |Riccardo et al. 2020 |
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|`mild_fraction_10_19`| 0.212|φ<sub>mild</sub>(10-19) | Fraction of infected individuals with mild symptoms, aged 10-19 |Riccardo et al. 2020 |
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|`mild_fraction_20_29`| 0.198|φ<sub>mild</sub>(20-29) | Fraction of infected individuals with mild symptoms, aged 20-29 |Riccardo et al. 2020 |
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|`mild_fraction_30_39`| 0.181|φ<sub>mild</sub>(30-39) | Fraction of infected individuals with mild symptoms, aged 30-39 |Riccardo et al. 2020 |
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|`mild_fraction_40_49`| 0.162|φ<sub>mild</sub>(40-49) | Fraction of infected individuals with mild symptoms, aged 40-49 |Riccardo et al. 2020 |
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|`mild_fraction_50_59`| 0.140|φ<sub>mild</sub>(50-59) | Fraction of infected individuals with mild symptoms, aged 50-59 |Riccardo et al. 2020 |
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|`mild_fraction_60_69`| 0.117|φ<sub>mild</sub>(60-69) | Fraction of infected individuals with mild symptoms, aged 60-69 |Riccardo et al. 2020 |
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|`mild_fraction_70_79`| 0.0906|φ<sub>mild</sub>(70-79) | Fraction of infected individuals with mild symptoms, aged 70-79 |Riccardo et al. 2020 |
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|`mild_fraction_80`| 0.0623|φ<sub>mild</sub>(80) | Fraction of infected individuals with mild symptoms, aged 80+ |Riccardo et al. 2020 |
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|`mild_infectious_factor`| 0.48 |*A<sub>mild</sub>*| Infectious rate of mildly symptomatic individuals relative to symptomatic individuals | Luo et al 2020 |
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|`mean_asymptomatic_to_recovery`| 15 |μ<sub>a,rec</sub> | Mean time from infection to recovery (and no longer infectious) for an asymptomatic individual (days) | Yang et al 2020 |
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|`sd_asymptomatic_to_recovery`| 5 |σ<sub>a,rec</sub> | Standard deviation from infection to recovery for an asymptomatic individual (days) | Yang et al 2020 |
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|`quarantine_length_traced_positive`| 14 | - | Maximum number of days quarantine for individuals who are traced after a contact tested positive | - |
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|`quarantine_length_positive`| 14 | - | Maximum number of days quarantine for individuals with a positive test result | - |
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|`quarantine_dropout_self`| 0.02 | - | Daily probability of drop out for an individual quarantining after self-reporting symptoms | - |
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|`quarantine_dropout_traced_symptoms`| 0.03| - | Daily probability of drop out for an individual quarantining after being traced following contact with an individual self-reporting symptoms | - |
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|`quarantine_dropout_traced_symptoms`| 0.04| - | Daily probability of drop out for an individual quarantining after being traced following contact with an individual self-reporting symptoms | - |
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|`quarantine_dropout_traced_positive`| 0.03 | - | Daily probability of drop out for an individual quarantining after being traced following contact with an individual who tested positive | - |
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|`quarantine_dropout_positive`| 0.02| - | Daily probability of drop out for an individual quarantining after a positive test result | - |
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|`quarantine_compliance_traced_symptoms`| 0.8| - | Fraction of individuals who initially comply with a quarantine notification after their contact reported symptoms | - |
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|`quarantine_dropout_positive`| 0.01| - | Daily probability of drop out for an individual quarantining after a positive test result | - |
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|`quarantine_compliance_traced_symptoms`| 0.5| - | Fraction of individuals who initially comply with a quarantine notification after their contact reported symptoms | - |
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|`quarantine_compliance_traced_positive`| 0.9 | - | Fraction of individuals who initially comply with a quarantine notification after their contact tested positive | - |
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|`test_on_symptoms`| 0 | - | Test individuals who show symptoms (0=no, 1=yes) | - |
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|`test_on_traced`| 0 | - | Test individuals who have been contact-traced (0=no, 1=yes) | - |
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|`test_release_on_negative`| 1 | - | Release individuals following a negative test (0=no, 1=yes) | - |
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|`trace_on_symptoms`| 0 | - | Trace contacts of individuals who show symptoms (0=no, 1=yes) | - |
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|`trace_on_positive`| 0 | - | Trace contacts of an individual who tests positive (0=no, 1=yes) | - |
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|`retrace_on_positive`| 0 | - | Repeat contract tracing be carried out on a positive test if already tested on symptoms (0=no, 1=yes) | - |
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|`retrace_on_positive`| 0 | - | Repeat contract tracing be carried out on a positive test if already traced on symptoms (0=no, 1=yes) | - |
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|`quarantine_on_traced`| 0 | - | Quarantine individuals who are traced (0=no, 1=yes) | - |
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|`traceable_interaction_fraction`| 0.8 | - | Fraction of interactions that are captured if both users have the app | - |
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|`tracing_network_depth`| 0 | - | Depth of interaction network to contact | - |
@@ -156,7 +156,7 @@
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|`test_insensitive_period`| 3 | - | Number of days following infection the test is insensitive | Woelfel et al. 2020 |
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|`test_sensitive_period`| 14 | - | Number of days following infection to end of period where test is sensitive | - |
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|`test_sensitivity`| 0.8 | - | Sensitivity of test in the time where it is sensitive | - |
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|`test_specificity`| 0.99| - | Specificity of test (at any time) | - |
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|`test_specificity`| 0.999| - | Specificity of test (at any time) | - |
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|`test_order_wait`| 1 | - | Minimum number of days to wait to take a test | - |
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|`test_order_wait_priority`| -1 | - | Minimum number of days to wait for a priority test to be taken | - |
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|`test_result_wait`| 1 | - | Number of days to wait for a test result | - |
Copy file name to clipboardexpand all lines: tests/data/baseline_parameters_transpose.csv
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@@ -19,8 +19,8 @@ elderly_network_adults,0.2,,Ratio of adults to elderly in work network for elder
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days_of_interactions,10,,Length of historic interactions traced (days),,Active intervention parameters
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end_time,200,,End time (total number of simulated days),,
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n_seed_infection,5,,Number of infections seeded at simulation start,,Infection parameters
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mean_infectious_period,6,μ,Mean of the generation time distribution (days),"Ma et al, 2020; Ganyani et al. 2020; Ferretti & Wymant et al. 2022",Infection parameters
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sd_infectious_period,2.5,σ,Standard deviation (days) of infectious period,"Ma et al, 2020; Ganyani et al. 2020; Ferretti & Wymant et al. 2022",Infection parameters
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mean_infectious_period,5.5,μ,Mean of the generation time distribution (days),"Ferretti et al in prep 2020; Ferretti & Wymant et al 2020; Xia et al 2020; He et al 2020; Cheng et al 2020",Infection parameters
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sd_infectious_period,2.14,σ,Standard deviation (days) of infectious period,"Ferretti et al in prep 2020; Ferretti & Wymant et al 2020; Xia et al 2020; He et al 2020; Cheng et al 2020",Infection parameters
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infectious_rate,5.64,*R*,Mean number of individuals infected by each infectious individual with moderate to severe symptoms,Derived from calibration,Infection parameters
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mean_time_to_symptoms,5.42,μ<sub>sym</sub>,Mean time from infection to onset of symptoms (days),McAloon et al.,Disease dynamics parameters
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sd_time_to_symptoms,2.7,σ<sub>sym</sub>,Standard deviation of time from infection to onset of symptoms (days),McAloon et al.,Disease dynamics parameters
@@ -31,25 +31,25 @@ mean_time_to_recover,12,μ<sub>rec</sub>,Mean time to recovery if hospitalis
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sd_time_to_recover,5,σ<sub>rec</sub>,Standard deviation of time to recovery if hospitalisaion is not required (days),Yang et al 2020,Disease dynamics parameters
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mean_time_to_death,11.74,μ<sub>death</sub>,Mean time to death after acquiring critical care (days),Personal communication with SPI-M; data soon to be published,Disease dynamics parameters
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sd_time_to_death,8.79,σ<sub>death</sub>,Standard deviation of time to death after acquiring critical care (days),Personal communication with SPI-M; data soon to be published,Disease dynamics parameters
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fraction_asymptomatic_0_9,0.16,φ<sub>asym</sub>(0-9),"Fraction of infected individuals who are asymptomatic, aged 0-9",Byambasuren et al. 2020,Disease dynamics parameters
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fraction_asymptomatic_10_19,0.16,φ<sub>asym</sub>(10-19),"Fraction of infected individuals who are asymptomatic, aged 10-19",Byambasuren et al. 2020,Disease dynamics parameters
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fraction_asymptomatic_20_29,0.16,φ<sub>asym</sub>(20-29),"Fraction of infected individuals who are asymptomatic, aged 20-29",Byambasuren et al. 2020,Disease dynamics parameters
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fraction_asymptomatic_30_39,0.16,φ<sub>asym</sub>(30-39),"Fraction of infected individuals who are asymptomatic, aged 30-39",Byambasuren et al. 2020,Disease dynamics parameters
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fraction_asymptomatic_40_49,0.16,φ<sub>asym</sub>(40-49),"Fraction of infected individuals who are asymptomatic, aged 40-49",Byambasuren et al. 2020,Disease dynamics parameters
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fraction_asymptomatic_50_59,0.16,φ<sub>asym</sub>(50-59),"Fraction of infected individuals who are asymptomatic, aged 50-59",Byambasuren et al. 2020,Disease dynamics parameters
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fraction_asymptomatic_60_69,0.16,φ<sub>asym</sub>(60-69),"Fraction of infected individuals who are asymptomatic, aged 60-69",Byambasuren et al. 2020,Disease dynamics parameters
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fraction_asymptomatic_70_79,0.16,φ<sub>asym</sub>(70-79),"Fraction of infected individuals who are asymptomatic, aged 70-79",Byambasuren et al. 2020,Disease dynamics parameters
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fraction_asymptomatic_80,0.16,φ<sub>asym</sub>(80),"Fraction of infected individuals who are asymptomatic, aged 80+",Byambasuren et al. 2020,Disease dynamics parameters
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fraction_asymptomatic_0_9,0.339,φ<sub>asym</sub>(0-9),"Fraction of infected individuals who are asymptomatic, aged 0-9",,Disease dynamics parameters
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fraction_asymptomatic_10_19,0.305,φ<sub>asym</sub>(10-19),"Fraction of infected individuals who are asymptomatic, aged 10-19",,Disease dynamics parameters
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fraction_asymptomatic_20_29,0.271,φ<sub>asym</sub>(20-29),"Fraction of infected individuals who are asymptomatic, aged 20-29",,Disease dynamics parameters
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fraction_asymptomatic_30_39,0.237,φ<sub>asym</sub>(30-39),"Fraction of infected individuals who are asymptomatic, aged 30-39",,Disease dynamics parameters
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fraction_asymptomatic_40_49,0.203,φ<sub>asym</sub>(40-49),"Fraction of infected individuals who are asymptomatic, aged 40-49",,Disease dynamics parameters
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fraction_asymptomatic_50_59,0.169,φ<sub>asym</sub>(50-59),"Fraction of infected individuals who are asymptomatic, aged 50-59",,Disease dynamics parameters
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fraction_asymptomatic_60_69,0.135,φ<sub>asym</sub>(60-69),"Fraction of infected individuals who are asymptomatic, aged 60-69",,Disease dynamics parameters
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fraction_asymptomatic_70_79,0.101,φ<sub>asym</sub>(70-79),"Fraction of infected individuals who are asymptomatic, aged 70-79",,Disease dynamics parameters
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fraction_asymptomatic_80,0.0667,φ<sub>asym</sub>(80),"Fraction of infected individuals who are asymptomatic, aged 80+",,Disease dynamics parameters
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asymptomatic_infectious_factor,0.29,*A<sub>asym</sub>*,Infectious rate of asymptomatic individuals relative to symptomatic individuals,Luo et al 2020,Infection parameters
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mild_fraction_0_9,0.79,φ<sub>mild</sub>(0-9),"Fraction of infected individuals with mild symptoms, aged 0-9",de Souza et al. 2020,Disease dynamics parameters
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mild_fraction_10_19,0.79,φ<sub>mild</sub>(10-19),"Fraction of infected individuals with mild symptoms, aged 10-19",de Souza et al. 2020,Disease dynamics parameters
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mild_fraction_20_29,0.73,φ<sub>mild</sub>(20-29),"Fraction of infected individuals with mild symptoms, aged 20-29","Yang, Lu et al. 2020",Disease dynamics parameters
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mild_fraction_30_39,0.68,φ<sub>mild</sub>(30-39),"Fraction of infected individuals with mild symptoms, aged 30-39","Yang, Lu et al. 2020",Disease dynamics parameters
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mild_fraction_40_49,0.65,φ<sub>mild</sub>(40-49),"Fraction of infected individuals with mild symptoms, aged 40-49","Yang, Lu et al. 2020",Disease dynamics parameters
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mild_fraction_50_59,0.59,φ<sub>mild</sub>(50-59),"Fraction of infected individuals with mild symptoms, aged 50-59","Yang, Lu et al. 2020",Disease dynamics parameters
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mild_fraction_60_69,0.53,φ<sub>mild</sub>(60-69),"Fraction of infected individuals with mild symptoms, aged 60-69","Yang, Lu et al. 2020",Disease dynamics parameters
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mild_fraction_70_79,0.41,φ<sub>mild</sub>(70-79),"Fraction of infected individuals with mild symptoms, aged 70-79","Yang, Lu et al. 2020",Disease dynamics parameters
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mild_fraction_80,0.27,φ<sub>mild</sub>(80),"Fraction of infected individuals with mild symptoms, aged 80+","Yang, Lu et al. 2020",Disease dynamics parameters
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mild_fraction_0_9,0.224,φ<sub>mild</sub>(0-9),"Fraction of infected individuals with mild symptoms, aged 0-9",Riccardo et al. 2020,Disease dynamics parameters
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mild_fraction_10_19,0.212,φ<sub>mild</sub>(10-19),"Fraction of infected individuals with mild symptoms, aged 10-19",Riccardo et al. 2020,Disease dynamics parameters
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mild_fraction_20_29,0.198,φ<sub>mild</sub>(20-29),"Fraction of infected individuals with mild symptoms, aged 20-29",Riccardo et al. 2020,Disease dynamics parameters
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mild_fraction_30_39,0.181,φ<sub>mild</sub>(30-39),"Fraction of infected individuals with mild symptoms, aged 30-39",Riccardo et al. 2020,Disease dynamics parameters
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mild_fraction_40_49,0.162,φ<sub>mild</sub>(40-49),"Fraction of infected individuals with mild symptoms, aged 40-49",Riccardo et al. 2020,Disease dynamics parameters
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mild_fraction_50_59,0.140,φ<sub>mild</sub>(50-59),"Fraction of infected individuals with mild symptoms, aged 50-59",Riccardo et al. 2020,Disease dynamics parameters
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mild_fraction_60_69,0.117,φ<sub>mild</sub>(60-69),"Fraction of infected individuals with mild symptoms, aged 60-69",Riccardo et al. 2020,Disease dynamics parameters
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mild_fraction_70_79,0.0906,φ<sub>mild</sub>(70-79),"Fraction of infected individuals with mild symptoms, aged 70-79",Riccardo et al. 2020,Disease dynamics parameters
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mild_fraction_80,0.0623,φ<sub>mild</sub>(80),"Fraction of infected individuals with mild symptoms, aged 80+",Riccardo et al. 2020,Disease dynamics parameters
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mild_infectious_factor,0.48,*A<sub>mild</sub>*,Infectious rate of mildly symptomatic individuals relative to symptomatic individuals,Luo et al 2020,Infection parameters
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mean_asymptomatic_to_recovery,15,"μ<sub>a,rec</sub>",Mean time from infection to recovery (and no longer infectious) for an asymptomatic individual (days),Yang et al 2020,Disease dynamics parameters
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sd_asymptomatic_to_recovery,5,"σ<sub>a,rec</sub>",Standard deviation from infection to recovery for an asymptomatic individual (days),Yang et al 2020,Disease dynamics parameters
@@ -126,17 +126,17 @@ quarantine_length_traced_symptoms,14,,Maximum number of days quarantine for indi
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quarantine_length_traced_positive,14,,Maximum number of days quarantine for individuals who are traced after a contact tested positive,,Active intervention parameters
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quarantine_length_positive,14,,Maximum number of days quarantine for individuals with a positive test result,,Active intervention parameters
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quarantine_dropout_self,0.02,,Daily probability of drop out for an individual quarantining after self-reporting symptoms,,Passive intervention parameters
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quarantine_dropout_traced_symptoms,0.03,,Daily probability of drop out for an individual quarantining after being traced following contact with an individual self-reporting symptoms,,Active intervention parameters
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quarantine_dropout_traced_symptoms,0.04,,Daily probability of drop out for an individual quarantining after being traced following contact with an individual self-reporting symptoms,,Active intervention parameters
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quarantine_dropout_traced_positive,0.03,,Daily probability of drop out for an individual quarantining after being traced following contact with an individual who tested positive,,Active intervention parameters
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quarantine_dropout_positive,0.02,,Daily probability of drop out for an individual quarantining after a positive test result,,Active intervention parameters
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quarantine_compliance_traced_symptoms,0.8,,Fraction of individuals who initially comply with a quarantine notification after their contact reported symptoms,,Active intervention parameters
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quarantine_dropout_positive,0.01,,Daily probability of drop out for an individual quarantining after a positive test result,,Active intervention parameters
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quarantine_compliance_traced_symptoms,0.5,,Fraction of individuals who initially comply with a quarantine notification after their contact reported symptoms,,Active intervention parameters
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quarantine_compliance_traced_positive,0.9,,Fraction of individuals who initially comply with a quarantine notification after their contact tested positive,,Active intervention parameters
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test_on_symptoms,0,,"Test individuals who show symptoms (0=no, 1=yes)",,Active intervention parameters
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test_on_traced,0,,"Test individuals who have been contact-traced (0=no, 1=yes)",,Active intervention parameters
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test_release_on_negative,1,,"Release individuals following a negative test (0=no, 1=yes)",,Active intervention parameters
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trace_on_symptoms,0,,"Trace contacts of individuals who show symptoms (0=no, 1=yes)",,Active intervention parameters
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trace_on_positive,0,,"Trace contacts of an individual who tests positive (0=no, 1=yes)",,Active intervention parameters
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retrace_on_positive,0,,"Repeat contract tracing be carried out on a positive test if already tested on symptoms (0=no, 1=yes)",,Active intervention parameters
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retrace_on_positive,0,,"Repeat contract tracing be carried out on a positive test if already traced on symptoms (0=no, 1=yes)",,Active intervention parameters
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quarantine_on_traced,0,,"Quarantine individuals who are traced (0=no, 1=yes)",,Active intervention parameters
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traceable_interaction_fraction,0.8,,Fraction of interactions that are captured if both users have the app,,Active intervention parameters
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tracing_network_depth,0,,Depth of interaction network to contact,,Active intervention parameters
@@ -152,9 +152,9 @@ quarantine_days,7,,The number of previous days' contacts to be traced and contac
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quarantine_smart_release_day,0,,Release a chain of quarantined people if after this number of days nobody has shown symptoms on the chain,,Active intervention parameters
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hospitalised_daily_interactions,0,,Daily random interactions of a hospitalised individual,,Passive intervention parameters
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test_insensitive_period,3,,Number of days following infection the test is insensitive,Woelfel et al. 2020,Active intervention parameters
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test_sensitive_period,14,,Number of days following infection to end of period where test is sensitive,,Active intervention parameters
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test_sensitivity,0.8,,Sensitivity of test in the time where it is sensitive,,Active intervention parameters
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test_specificity,0.99,,Specificity of test (at any time),,Active intervention parameters
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test_sensitive_period,14,,Number of days following infection to end of period where test is sensitive,,Active intervention parameters
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test_sensitivity,0.8,,Sensitivity of test in the time where it is sensitive,,Active intervention parameters
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test_specificity,0.999,,Specificity of test (at any time),,Active intervention parameters
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test_order_wait,1,,Minimum number of days to wait to take a test,,Active intervention parameters
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test_order_wait_priority,-1,,Minimum number of days to wait for a priority test to be taken,,
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test_result_wait,1,,Number of days to wait for a test result,,Active intervention parameters
np.testing.assert_equal( len( df_neg) >100, True, "In-sufficient household member with negative test results" )
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np.testing.assert_equal( sum( df_neg["has_token"] !=True ), 0, "Household members lose their token on a negative result despite positive household member" )
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np.testing.assert_equal( sum( df_neg["quarantined"]==0), 0, "Household members released from quarantine despite positive household member" )
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