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DeshanPereraDeshanPerera
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default_parameters_file
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‎default_Parameter_Files_Apollo/parameters_Example/individual_Profiles/all_Profiles/profile_1.json‎

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{
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"Profile name":"Adults Medicated",
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"Probability of occurence":"0.75",
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# Sampled individuals can be REMOVED from the infectious population or become LESS INFECTIOUS or NO CHANGE to infectivity
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"Sampling effect":"No change",
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"Sampling less infectious effect Alpha":"5",
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"Sampling less infectious effect Beta":"10",
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# TERMINAL AND INFECTIOUS AMOUNTS
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"Infectious load distribution type":"Fixed",
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"Infectious load Binomial trials":1000,
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"Infectious load Binomial probability":"0.75",
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"Infectious load Fixed":1,
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"Terminal load distribution type":"Fixed",
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"Terminal load Binomial trials":100000,
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"Terminal load Binomial probability":"0.75",
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"Terminal load Fixed":1000,
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# Control the number of hosts being infected
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"Infection sequence distribution":"Fixed",
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"Infection sequence Binomial trials":2,
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"Infection sequence Binomial probability":"0.5",
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"Infection sequence Fixed":2,
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"Tissue profiles":{
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"Tissue 1":{
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"Cell limit":"YES",
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"Cell limit Binomial trials":100000,
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"Cell limit Binomial probability":"0.50",
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"Viral distribution type":"Binomial",
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"Viral distribution Binomial trials":10,
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"Viral distribution Binomial probability":"0.5",
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"Viral distribution Gamma shape":"3",
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"Viral distribution Gamma scale":"3.33",
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"Replication phases":{
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"Number of phases":1,
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"Phase 1 Mode":"Neutral",
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"Phase 1 Time ratio":"1",
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"Phase 1 Variance":"100",
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"Phase 1 Alpha":"100",
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"Phase 1 Beta":"100",
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},
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},
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"Tissue 2":{
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"Cell limit":"No",
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"Cell limit Binomial trials":100000,
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"Cell limit Binomial probability":"0.10",
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"Viral distribution type":"Binomial",
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"Viral distribution Binomial trials":10,
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"Viral distribution Binomial probability":"0.5",
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"Replication phases":{
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"Number of phases":1,
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"Phase 1 Mode":"Depriciation",
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"Phase 1 Time ratio":"1",
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"Phase 1 Alpha":"100",
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"Phase 1 Beta":"100",
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},
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},
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"Tissue 3":{
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"Cell limit":"Yes",
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"Cell limit Binomial trials":100000,
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"Cell limit Binomial probability":"0.10",
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"Viral distribution type":"Binomial",
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"Viral distribution Binomial trials":10,
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"Viral distribution Binomial probability":"0.5",
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"Replication phases":{
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"Number of phases":1,
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"Phase 1 Mode":"Stationary",
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"Phase 1 Time ratio":"1",
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"Phase 1 Variance":"100",
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},
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},
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},
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}

‎default_Parameter_Files_Apollo/parameters_Example/individual_Profiles/all_Profiles/profile_2.json‎

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{
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"Profile name":"Children",
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"Probability of occurence":"0.15",
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# Sampled individuals can be REMOVED from the infectious population or become LESS INFECTIOUS or NO CHANGE to infectivity
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"Sampling effect":"No change",
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"Sampling less infectious effect Alpha":"5",
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"Sampling less infectious effect Beta":"10",
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# TERMINAL AND INFECTIOUS AMOUNTS
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"Infectious load distribution type":"Fixed",
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"Infectious load Binomial trials":100,
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"Infectious load Binomial probability":"0.75",
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"Infectious load Fixed":1,
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"Terminal load distribution type":"Fixed",
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"Terminal load Binomial trials":100000,
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"Terminal load Binomial probability":"0.75",
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"Terminal load Fixed":1000,
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# Control the number of hosts that will be infected
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"Infection sequence distribution":"Fixed",
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"Infection sequence Binomial trials":2,
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"Infection sequence Binomial probability":"0.5",
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"Infection sequence Fixed":2,
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"Tissue profiles":{
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"Tissue 1":{
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"Cell limit":"YES",
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"Cell limit Binomial trials":100000,
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"Cell limit Binomial probability":"0.50",
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"Viral distribution type":"Gamma",
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"Viral distribution Binomial trials":10,
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"Viral distribution Binomial probability":"0.5",
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"Viral distribution Gamma shape":"3",
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"Viral distribution Gamma scale":"3.33",
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"Replication phases":{
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"Number of phases":1,
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"Phase 1 Mode":"Neutral",
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"Phase 1 Time ratio":"1",
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"Phase 1 Variance":"100",
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"Phase 1 Alpha":"100",
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"Phase 1 Beta":"100",
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},
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},
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"Tissue 2":{
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"Cell limit":"No",
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"Cell limit Binomial trials":100000,
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"Cell limit Binomial probability":"0.10",
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"Viral distribution type":"Binomial",
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"Viral distribution Binomial trials":10,
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"Viral distribution Binomial probability":"0.5",
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"Viral distribution Gamma shape":"3",
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"Viral distribution Gamma scale":"3.33",
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"Replication phases":{
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"Number of phases":1,
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"Phase 1 Mode":"Stationary",
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"Phase 1 Time ratio":"1",
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"Phase 1 Variance":"100",
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},
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},
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"Tissue 3":{
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"Cell limit":"NO",
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"Cell limit Binomial trials":100000,
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"Cell limit Binomial probability":"0.10",
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"Viral distribution type":"Binomial",
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"Viral distribution Binomial trials":10,
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"Viral distribution Binomial probability":"0.5",
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"Viral distribution Gamma shape":"3",
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"Viral distribution Gamma scale":"3.33",
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"Replication phases":{
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"Number of phases":3,
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"Phase 1 Mode":"Neutral",
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"Phase 1 Time ratio":"0.2",
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"Phase 2 Mode":"Stationary",
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"Phase 2 Time ratio":"0.5",
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"Phase 2 Variance":"100",
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"Phase 3 Mode":"Depriciation",
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"Phase 3 Time ratio":"0.3",
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"Phase 3 Alpha":"100",
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"Phase 3 Beta":"100",
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},
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},
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},
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}

‎default_Parameter_Files_Apollo/parameters_Example/individual_Profiles/all_Profiles/profile_3.json‎

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{
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"Profile name":"Adults Normal",
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"Probability of occurence":"0.10",
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# Sampled individuals can be REMOVED from the infectious population or become LESS INFECTIOUS or NO CHANGE to infectivity
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"Sampling effect":"Less infectious",
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"Sampling less infectious effect Alpha":"5",
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"Sampling less infectious effect Beta":"10",
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# TERMINAL AND INFECTIOUS AMOUNTS
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"Infectious load distribution type":"Fixed",
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"Infectious load Binomial trials":100,
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"Infectious load Binomial probability":"0.75",
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"Infectious load Fixed":1,
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"Terminal load distribution type":"Fixed",
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"Terminal load Binomial trials":100000,
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"Terminal load Binomial probability":"0.75",
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"Terminal load Fixed":100,
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# Control the viral transmission infection from one host to another
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"Infection sequence distribution":"Fixed",
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"Infection sequence Binomial trials":2,
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"Infection sequence Binomial probability":"0.5",
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"Infection sequence Fixed":2,
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"Tissue profiles":{
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"Tissue 1":{
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"Cell limit":"NO",
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"Cell limit Binomial trials":100000,
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"Cell limit Binomial probability":"0.50",
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"Viral distribution type":"Binomial",
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"Viral distribution Binomial trials":10,
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"Viral distribution Binomial probability":"0.5",
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"Viral distribution Gamma shape":"3",
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"Viral distribution Gamma scale":"3.33",
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"Replication phases":{
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"Number of phases":1,
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"Phase 1 Mode":"Neutral",
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"Phase 1 Time ratio":"1",
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"Phase 1 Variance":"100",
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"Phase 1 Alpha":"100",
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"Phase 1 Beta":"100",
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},
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},
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"Tissue 2":{
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"Cell limit":"Yes",
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"Cell limit Binomial trials":100000,
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"Cell limit Binomial probability":"0.10",
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"Viral distribution type":"Binomial",
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"Viral distribution Binomial trials":10,
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"Viral distribution Binomial probability":"0.5",
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"Viral distribution Gamma shape":"3",
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"Viral distribution Gamma scale":"3.33",
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"Replication phases":{
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"Number of phases":1,
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"Phase 1 Mode":"Stationary",
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"Phase 1 Time ratio":"1",
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"Phase 1 Variance":"100",
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},
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},
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"Tissue 3":{
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"Cell limit":"NO",
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"Cell limit Binomial trials":100000,
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"Cell limit Binomial probability":"0.10",
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"Viral distribution type":"Binomial",
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"Viral distribution Binomial trials":10,
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"Viral distribution Binomial probability":"0.5",
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"Viral distribution Gamma shape":"3",
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"Viral distribution Gamma scale":"3.33",
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"Replication phases":{
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"Number of phases":3,
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"Phase 1 Mode":"Neutral",
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"Phase 1 Time ratio":"0.2",
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"Phase 2 Mode":"Stationary",
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"Phase 2 Time ratio":"0.5",
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"Phase 2 Variance":"100",
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"Phase 3 Mode":"Depriciation",
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"Phase 3 Time ratio":"0.3",
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"Phase 3 Alpha":"100",
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"Phase 3 Beta":"100",
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},
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},
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},
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}

‎default_Parameter_Files_Apollo/parameters_Example/individual_Profiles/node_Master.json‎

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{
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# In days the time taken for viral replication, from cell entry to progeny generation
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"Shape replication time":"20.0",
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"Scale replication time":"0.020",
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# In days the time the virus will spend in the host, if unaffected
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"Shape days in host":"20.0",
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"Scale days in host":"0.27",
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"Sampling present":"Yes",
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# If Resampling is YES, then the same node can be sampled multiple times as long as it is not removed.
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"Resampling of nodes":"Yes",
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"Sampling rate Binomial trials":2,
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"Sampling rate Binomial probability":"0.75",
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"Distribution per node sequences sampled":"FIXED",
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"Per node sampling rate Binomial trials":2,
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"Per node sampling rate Binomial probability":"0.5",
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"Per node sampling rate Fixed":1,
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# Control if the simulation ends via the max sampled sequences or not
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"Limit samples obtained":"Yes",
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"Max samples to obtain":20,
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"Limit infected hosts":"No",
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"Host limit":2,
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# Number of progeny that will be generated by a reference virulant particle
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# Negative Binomial, Gamma, Poisson
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"Progeny distribution type":"Negative Binomial",
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"Progeny Negative Binomial sucesses":10,
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"Progeny Negative Binomial probability":"0.55",
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"Progeny Poisson mean":"10",
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"Progeny Gamma shape":"10",
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"Progeny Gamma scale":"0.5",
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# Infected individuals can remain suceptible to infection if set to YES, else they will be removed if their viral load goes to zero
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"Infected to Recovered":"No",
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"Number of node profiles":3,
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"Location of node profiles":"parameters_Example/individual_Profiles/all_Profiles",
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"Tissue profiles":{
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"Number of tissues":3,
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"Tissue 1 Name":"Blood",
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"Tissue 2 Name":"Lung",
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"Tissue 3 Name":"Gut",
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"Viral entry tissues":"1,2",
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"Infectious load tissues":"1",
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"Terminal load tissues":"1,2,3",
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"Viral exit tissues":"1",
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"Sampling tissues":"1,2,3",
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"Viral tissue migration":"Yes",
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"Viral migration":{
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"1_2":{
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"Start generation":2,
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"Viral migration Binomial trials":100,
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"Viral migration Binomial probability":"0.10",
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},
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"2_1":{
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"Start generation":10,
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"Viral migration Binomial trials":100,
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"Viral migration Binomial probability":"0.10",
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},
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"2_3":{
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"Start generation":10,
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"Viral migration Binomial trials":50,
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"Viral migration Binomial probability":"0.01",
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},
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"3_1":{
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"Start generation":2,
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"Viral migration Binomial trials":10,
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"Viral migration Binomial probability":"0.9",
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},
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},
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}
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}

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