Simulation of pandemic spread - Revision history

Kopd05: /* NetLogo File */

2024-01-16T21:28:52Z

‎NetLogo File

Kopd05: /* NetLogo File */

2024-01-16T21:26:06Z

‎NetLogo File

Kopd05: /* Conclusion */

2024-01-16T21:24:00Z

‎Conclusion

Kopd05: /* Conclusion */

2024-01-16T21:23:02Z

‎Conclusion

Kopd05: /* Results */

2024-01-16T21:18:28Z

‎Results

Kopd05: /* Predefined viruses */

2024-01-16T20:54:58Z

‎Predefined viruses

Kopd05: /* Predefined viruses */

2024-01-16T20:50:33Z

‎Predefined viruses

Kopd05: /* UI */

2024-01-16T20:00:13Z

‎UI

Kopd05: /* UI */

2024-01-16T20:00:03Z

‎UI

Kopd05: /* UI */

2024-01-16T19:59:38Z

‎UI

@@ Line 130: / Line 130: @@
 =NetLogo File=
-Below I attach the source file together with the map of the Czech Republic, which must be in the same directory as the NetLogo source file.
+Below I attach the source file together with the map of the Czech Republic, which must be in the same directory as the NetLogo source file.<br>
 =Sources=
 <references/>

@@ Line 130: / Line 130: @@
 =NetLogo File=
 =Sources=
 <references/>

@@ Line 127: / Line 127: @@
 =Conclusion=
-The model in this simplified version can simulate the development of various pandemics within the Czech Republic. Its main advantage is the limitation of the territory that follows the borders of the Czech Republic and also the preset values for different viruses, which are based on real data. We must also not forget the customization option, thanks to which the user can create tailor-made virus simulations. Creating the model itself was not as challenging as searching for all the background information for each virus.
+The model in this simplified version can simulate the development of various pandemics within the Czech Republic. Its main advantage is the limitation of the territory that follows the borders of the Czech Republic and also the preset values for different viruses, which are based on real data. We must also not forget the customization option, thanks to which the user can create tailor-made virus simulations. Creating the model itself was not as challenging as searching for all the background information for each virus. As part of the extension, it would be possible to add additional predefined viruses or to add additional refinement parameters that would affect the course of the entire simulation for a given virus.
 =NetLogo File=

← Older revision		Revision as of 21:23, 16 January 2024
Line 127:		Line 127:

	=Conclusion=		=Conclusion=
		+	The model in this simplified version can simulate the development of various pandemics within the Czech Republic. Its main advantage is the limitation of the territory that follows the borders of the Czech Republic and also the preset values for different viruses, which are based on real data. We must also not forget the customization option, thanks to which the user can create tailor-made virus simulations. Creating the model itself was not as challenging as searching for all the background information for each virus.

	=NetLogo File=		=NetLogo File=

← Older revision		Revision as of 21:18, 16 January 2024
Line 118:		Line 118:

	=Results=		=Results=
		+	Here we can see on the graph the results for the individual diseases that are selected, with the quarantine effort set to 0.2 and the capacity of the health facilities also set to 0.2.<br>
		+	<gallery mode="packed-hover">
		+	Image:Covid19.png\|''(Covid19)''
		+	Image:Measles.png\|''(Measles)''
		+	Image:Ebola.png\|''(Ebola)''
		+	</gallery>
		+	For all simulation results shown above, the default settings for the selected virus were used. The population was set to 501, the number of infected individuals to 19, and the number of individuals with immunity to 0.

	=Conclusion=		=Conclusion=

@@ Line 60: / Line 60: @@
 '''Fatality rate = 0.000005'''<ref>Center for Disease Control and Prevention., 2023. Preliminary estimated influenza-related illnesses, medical visits, hospitalizations, and deaths in the United States – 2021-2022 influenza season. Centers for Disease Control and Prevention [online] [vid. 11. leden 2024]. Získáno z: https://www.cdc.gov/flu/about/burden/2021-2022.htm
 </ref><br>
-'''Recovery rate = 7'''<ref>WHO, nedatováno. Influenza (seasonal). World Health Organization [online] [vid. 16. leden 2024]. Získáno z: https://www.who.int/news-room/fact-sheets/detail/influenza-(seasonal)</ref>
+'''Recovery rate = 7'''<ref>WHO, nedatováno. Influenza (seasonal). World Health Organization [online] [vid. 16. leden 2024]. Získáno z: https://www.who.int/news-room/fact-sheets/detail/influenza-(seasonal)</ref><br>
 '''Immunity = False''' (own experience :-) )

@@ Line 44: / Line 44: @@
 Covid-19, caused by the novel coronavirus SARS-CoV-2, emerged in late 2019 and quickly developed into a global pandemic. It primarily spreads through respiratory droplets, causing a range of symptoms from mild respiratory issues to severe pneumonia, with a heightened risk for older adults and those with underlying health conditions. <br>
 '''R0 = 0.71''' <ref>COVDATA. [online]. [citováno: 11.1.2024]. Dostupné z: https://www.covdata.cz/cesko.php</ref><br>
-'''Fatality rate = 0.0004''' <ref>Edouard Mathieu, Hannah Ritchie, Lucas Rodés-Guirao, Cameron Appel, Charlie Giattino, Joe Hasell, Bobbie Macdonald, Saloni Dattani, Diana Beltekian, Esteban Ortiz-Ospina and Max Roser (2020) - "Coronavirus Pandemic (COVID-19)". Published online at OurWorldInData.org. Retrieved from: 'https://ourworldindata.org/coronavirus' [Online Resource]</ref>
+'''Fatality rate = 0.0004''' <ref>Edouard Mathieu, Hannah Ritchie, Lucas Rodés-Guirao, Cameron Appel, Charlie Giattino, Joe Hasell, Bobbie Macdonald, Saloni Dattani, Diana Beltekian, Esteban Ortiz-Ospina and Max Roser (2020) - "Coronavirus Pandemic (COVID-19)". Published online at OurWorldInData.org. Retrieved from: 'https://ourworldindata.org/coronavirus' [Online Resource]</ref><br>
 ===Spanish Influenza===
 The Spanish Influenza, which occurred in 1918, was an exceptionally deadly H1N1 influenza A virus that caused a devastating pandemic.<br>
 '''R0 = 1.2 - 3.0''' <ref>Emilia Vynnycky, Amy Trindall, Punam Mangtani, Estimates of the reproduction numbers of Spanish influenza using morbidity data, International Journal of Epidemiology, Volume 36, Issue 4, August 2007, Pages 881–889, https://doi.org/10.1093/ije/dym071</ref><br>
-'''Fatality rate = 0.03''' <ref>Taubenberger, J. K., & Morens, D. M. (2006). 1918 Influenza: the Mother of All Pandemics. Emerging Infectious Diseases, 12(1), 15-22. https://doi.org/10.3201/eid1201.050979.</ref>
+'''Fatality rate = 0.03''' <ref>Taubenberger, J. K., & Morens, D. M. (2006). 1918 Influenza: the Mother of All Pandemics. Emerging Infectious Diseases, 12(1), 15-22. https://doi.org/10.3201/eid1201.050979.</ref><br>
 ===Seasonal Influenza===
 Seasonal Influenza, or the flu, is an annual respiratory illness caused by influenza viruses. It typically circulates during the colder months and can lead to fever, cough, and muscle aches.<br>
 '''RO = 0.9 - 2.1''' <ref>EISENBERG, Joseph, 2020. R0: How scientists quantify the intensity of an outbreak like coronavirus and its pandemic potential: The pursuit: University of Michigan School of Public Health: Coronavirus: Pandemic. R0: How Scientists Quantify the Intensity of an Outbreak Like Coronavirus and Its Pandemic Potential | The Pursuit | University of Michigan School of Public Health | Coronavirus | Pandemic [online] [vid. 11. leden 2024]. Získáno z: https://sph.umich.edu/pursuit/2020posts/how-scientists-quantify-outbreaks.html</ref><br>
 '''Fatality rate = 0.000005'''<ref>Center for Disease Control and Prevention., 2023. Preliminary estimated influenza-related illnesses, medical visits, hospitalizations, and deaths in the United States – 2021-2022 influenza season. Centers for Disease Control and Prevention [online] [vid. 11. leden 2024]. Získáno z: https://www.cdc.gov/flu/about/burden/2021-2022.htm
-</ref>
+</ref><br>
 ===Measles===
 Measles is a highly contagious viral infection, primarily affecting children, characterized by a distinctive rash and fever.<br>
 '''R0 = 12-18'''<ref>Guerra, F. M., Bolotin, S., Lim, G., Heffernan, J., Deeks, S. L., Li, Y., & Crowcroft, N. S. (2017). The basic reproduction number (R0) of measles: a systematic review. The Lancet. Infectious diseases, 17(12), e420–e428. https://doi.org/10.1016/S1473-3099(17)30307-9</ref><br>
-'''Fatality rate = 0.001'''<ref>CENTERS FOR DISEASE CONTROL AND PREVENTION, 2019. Measles. Centers for Disease Control and Prevention [online] [vid. 11. leden 2024]. Získáno z: https://www.cdc.gov/globalhealth/newsroom/topics/measles/index.html </ref>
+'''Fatality rate = 0.001'''<ref>CENTERS FOR DISEASE CONTROL AND PREVENTION, 2019. Measles. Centers for Disease Control and Prevention [online] [vid. 11. leden 2024]. Získáno z: https://www.cdc.gov/globalhealth/newsroom/topics/measles/index.html </ref><br>
 ===SARS===
 SARS (Severe Acute Respiratory Syndrome) emerged in 2002, caused by a coronavirus (SARS-CoV), resulting in severe respiratory distress.<br>
 '''R0 = 2.7'''<ref>CHAN‐YEUNG, Moira a Rui‐Heng XU, 2003. SARS: epidemiology [online]. listopad 2003. B.m.: Wiley. Dostupné z: doi:10.1046/j.1440-1843.2003.00518.x</ref><br>
-'''Fatality rate = 0.096'''<ref>CHAN‐YEUNG, Moira a Rui‐Heng XU, 2003. SARS: epidemiology [online]. listopad 2003. B.m.: Wiley. Dostupné z: doi:10.1046/j.1440-1843.2003.00518.x</ref>
+'''Fatality rate = 0.096'''<ref>CHAN‐YEUNG, Moira a Rui‐Heng XU, 2003. SARS: epidemiology [online]. listopad 2003. B.m.: Wiley. Dostupné z: doi:10.1046/j.1440-1843.2003.00518.x</ref><br>
+'''Recovery rate = 10-14''' <ref>CENTERS FOR DISEASE CONTROL AND PREVENTION, 2005. SARS. Centers for Disease Control and Prevention [online] [vid. 16. leden 2024]. Získáno z: https://www.cdc.gov/sars/about/faq.html</ref><br>
 ===Ebola===
 Ebola, a severe and often fatal viral hemorrhagic fever, gained global attention during outbreaks in Africa. It causes internal bleeding and multiple organ failure, with a high mortality rate.<br>
 '''R0 = 1.95'''<ref>Muzembo, B. A., Kitahara, K., Mitra, D., Ntontolo, N. P., Ngatu, N. R., Ohno, A., Khatiwada, J., Dutta, S., & Miyoshi, S. I. (2024). The basic reproduction number (R0) of ebola virus disease: A systematic review and meta-analysis. Travel medicine and infectious disease, 102685. Advance online publication. https://doi.org/10.1016/j.tmaid.2023.102685</ref><br>
-'''Fatality rate = 0.5'''<ref>Patel PR, Shah Su. Ebola Virus. [Updated 2023 Jul 17]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK560579/</ref>
+'''Fatality rate = 0.5'''<ref>Patel PR, Shah Su. Ebola Virus. [Updated 2023 Jul 17]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK560579/</ref><br>
 =Variables=

@@ Line 93: / Line 93: @@
 =UI=
 The user interface consists of setup and go buttons. These are used to prepare all necessary data and values before starting the simulation and to start or pause the simulation itself.<br>
 A switch that enables/disables immunity, which affects whether individuals in the simulation can be immune to the virus after they have recovered from it.<br>
@@ Line 98: / Line 99: @@
 The population slider sets the initial number of individuals that appear in the simulation. We can choose from values 1-1000.<br>
 Slider to set the initial infected individuals.<br>
-A slider to set the rate at which individuals heal.<br>[[File:Pandemic_spread_ui.png|thumb]]
+A slider to set the rate at which individuals heal.<br>
 Slider to set the initial state of immune individuals.<br>
 Quarantine effort, which tells us how individuals are trying to comply with the quarantine.<br>

← Older revision		Revision as of 19:59, 16 January 2024
Line 93:		Line 93:

	=UI=		=UI=
		+	The user interface consists of setup and go buttons. These are used to prepare all necessary data and values before starting the simulation and to start or pause the simulation itself.<br>
		+	A switch that enables/disables immunity, which affects whether individuals in the simulation can be immune to the virus after they have recovered from it.<br>
		+	Also from various sliders that set the values of variables that are then used within the simulation run.<br>
		+	The population slider sets the initial number of individuals that appear in the simulation. We can choose from values 1-1000.<br>
		+	Slider to set the initial infected individuals.<br>
		+	A slider to set the rate at which individuals heal.<br>
		+	Slider to set the initial state of immune individuals.<br>
		+	Quarantine effort, which tells us how individuals are trying to comply with the quarantine.<br>
		+	The transmission rate of the virus between individuals.<br>
		+	The mortality rate of the virus when an individual is infected with it.<br>
		+	And the capacity of health facilities, which is reflected in the rate of spread of the virus if it is exceeded.<br>
		+
		+	[[File:Pandemic_spread_ui.png\|thumb]]

	=Results=		=Results=