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Epidemic Network
Experimental environment for testing of large array of theoretical conditions for development epidemic event within various quantitative, spatial and connectedness (network structure) aspects.
1
mention
2
contributors
Description
See full list of documentation resources in documentation.
Inputs
| Name | Type | Description |
|---|---|---|
| seed | integer | random generator seed number used as random-seed seed. |
| initial-households | integer | initial count of households. |
| population-coefficient | integer | household size variance coefficient (mean of exponential distribution). |
| initial-clusters | integer | initial count of clusters/settlements. |
| cluster-radius-min, cluster-radius-max | integer | minimum/maximum cluster radius used to sample a random cluster radius from an uniform distribution, as in-radius (min-cluster-radius + (random max-cluster-radius)). |
| search-radius | integer | maximum search distance to establish links. |
| max-connections | integer | maximum number of connections (links) per distance range. |
| initial-infected | integer | number of initial cases or people agents initialised with the "incubation" stage and a stochastic state of stage 1 counter. |
| max-daily-contacts | integer | maximum number of connections to be considered contacts each day. |
| duration-latent-mean, duration-latent-stddev | float | Mean and standard deviation of duration of the latent stage of the disease, used in random-normal duration-latent-mean duration-latent-stddev. |
| duration-prodromal-mean, duration-prodromal-stddev | float | Mean and standard deviation of duration of the prodromal stage of the disease, used in random-normal duration-prodromal-mean duration-prodromal-stddev. |
| duration-contagious-mean, duration-contagious-stddev | float | Mean and standard deviation of duration of the contagious stage of the disease, used in random-normal duration-contagious-mean duration-contagious-stddev. |
| mortality-rate | float | Average mortality rate applied to all individuals (people) in the population. |
| transmission-prob-range1-mean, transmission-prob-range1-stddev | float | Mean and standard deviation of transmission probability towards people within range 1 (search-radius * 0.125), used in random-normal transmission-prob-range1-mean transmission-prob-range1-stddev. |
| transmission-prob-range2-mean, transmission-prob-range2-stddev | float | Mean and standard deviation of transmission probability towards people within range 2 (search-radius * 0.25), used in random-normal transmission-prob-range2-mean transmission-prob-range2-stddev. |
| transmission-prob-range3-mean, transmission-prob-range3-stddev | float | Mean and standard deviation of transmission probability towards people within range 3 (search-radius * 0.5), used in random-normal transmission-prob-range3-mean transmission-prob-range3-stddev. |
| transmission-prob-range4-mean, transmission-prob-range4-stddev | float | Mean and standard deviation of transmission probability towards people within range 4 (search-radius), used in random-normal transmission-prob-range4-mean transmission-prob-range4-stddev. |
| range1-search-radius-share, range2-search-radius-share, range3-search-radius-share, range4-search-radius-share | float | the proportion of search-radius effective for each transmission range. |
| range1-initial-connections-share, range2-initial-connections-share, range3-initial-connections-share, range4-initial-connections-share | float | the proportion of max-connections from which a random sample is taken as initial contacts of the infected people for each distance range. |
Outputs
| Name | Type | Description |
|---|---|---|
| pos-spread | integer | Count of positive disease transmission encounter of an individual (passed to other person) |
| neg-spread | integer | Count of negative disease transmission encounter of an individual (not passed to other person) |
| count-spread | integer | Cumulative number of daily contacts |
| count-daily-contact | integer | Sum of all daily contacts for the actual day (reset each day) |
| count-daily-transmission | integer | Sum of all daily disease transmission encounter for the actual day (reset each day) |
| count-daily-transmission-pers | integer | Number of people with the potential to performing a disease transmission encounter for the actual day (reset each day) |
| nw-betcen | float | Network metrics':' betweenness centrality |
| nw-eigcen | float | Network metrics':' eigenvector centrality |
| nw-clocen | float | Network metrics':' closeness centrality |
| nw-clucoe | float | Network metrics':' clustering coefficient |
| nw-mod | float | Network metrics':' modularity |
Mentions
Contributors
MV
Marek Vlach
Author, Copyright Holder, Creator
AA
Andreas Angourakis
Contributor
Member of community
