COVID-19 symptoms - Revision history

Stek15 at 13:43, 20 January 2021

2021-01-20T13:43:38Z

Stek15 at 13:41, 20 January 2021

2021-01-20T13:41:29Z

Stek15 at 13:22, 20 January 2021

2021-01-20T13:22:14Z

Stek15 at 13:10, 20 January 2021

2021-01-20T13:10:08Z

Stek15 at 13:04, 20 January 2021

2021-01-20T13:04:18Z

Stek15 at 12:58, 20 January 2021

2021-01-20T12:58:09Z

Stek15 at 12:27, 20 January 2021

2021-01-20T12:27:16Z

Stek15 at 12:25, 20 January 2021

2021-01-20T12:25:55Z

Stek15 at 12:21, 20 January 2021

2021-01-20T12:21:55Z

Stek15 at 12:19, 20 January 2021

2021-01-20T12:19:04Z

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 Expanding the model using specific weights for the individual links between symptoms, if such are discovered during the ongoing COVID-19 research, could also bear very interesting fruits.
-=7. Code=
+=6. Code=
 [[File:Covid-19 symptoms.nlogo]]

@@ Line 1: / Line 1: @@
 {{DISPLAYTITLE: Covid-19 symptoms simulation (NetLogo)}}
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 The main issue has, obviously, been data collection. As has been stated under Problem definition, the current sources are not only scarce, but also unreliable. However, I do believe that the positive side of my simulation is that it may be easily adjusted (symptoms added, thresholds edited, ''suspected-positivity-line'' moved, etc.) once we learn more about the disease. For now it may serve as a skeleton and, frankly, may be quite as reliable for the purposes of self-diagnosis as many of the suspiciously expensive home-testing kits available online.
-To improve the model, it would be good to
+Expanding the model using specific weights for the individual links between symptoms, if such are discovered during the ongoing COVID-19 research, could also bear very interesting fruits.
 =7. Code=
 =Sources=
-WebMD. (2021). Signs of Coronavirus (COVID-19). [online] Available at: https://www.webmd.com/lung/covid-19-symptoms#1.
+WebMD. (2021). Signs of Coronavirus (COVID-19). [online] Available at: [https://www.webmd.com/lung/covid-19-symptoms#1].
 Health Service Executive, Ireland. (2021). Symptoms of coronavirus. [online] Available at: https://www2.hse.ie/conditions/coronavirus/symptoms.html.

@@ Line 12: / Line 12: @@
 We are all familiar with the present pandemic situation. One of the main factors of the financial impact of the disease is the need for testing. Be it individual or nation-wide, the time, resources, and personnel required are far beyond what could be manageable long-term. Securely identifying the symptoms and tracking them could allow for more accurate quarantine measures.
-The available information on the COVID-19 disease is being constantly updated and developed. To take this into consideration, the model was created to be adaptable and easily editable. Even during the course of model creation, which only took a couple of weeks, the most commonly listed symptoms have been updated based on newly available information several times. The final list of 7 of the most common symptoms among patients hospitalized with COVID-19 as stated by Chinese researchers has been taken from https://www.webmd.com/lung/covid-19-symptoms#1.
+The available information on the COVID-19 disease is being constantly updated and developed. To take this into consideration, the model was created to be adaptable and easily editable. Even during the course of model creation, which only took a couple of weeks, the most commonly listed symptoms have been updated based on newly available information several times. The final list of 7 of the most common symptoms among patients hospitalized with COVID-19 as stated by Chinese researchers has been taken from WebMD (2021).
-The table below lists said symptoms, their percentual incidence in patients hospitalized with COVID-19, and the added probability '''P(A∪B∪C)''' of occurrence in any sick patient (considering COVID-19, the common cold, and the flu), calculated from data taken from https://www2.hse.ie/conditions/coronavirus/symptoms.html).
+The table below lists said symptoms, their percentual incidence in patients hospitalized with COVID-19, and the added probability '''P(A∪B∪C)''' of occurrence in any sick patient (considering COVID-19, the common cold, and the flu), calculated from data taken from Health Service Executive, Ireland (2021).
 [[File:Stek15-table1.png]]
@@ Line 61: / Line 61: @@
 [[File:Stek15-results2.png]]
-We can see that not only the symptoms developed much faster (we were already able to diagnose the lady at about 2 ticks), but the development has also been much steeper, causing the lady to experience almost all of the 7 main symptoms for the majority of the time. Hopefully, she got all better soon.
+We can see that not only the symptoms developed much faster (we were already able to first diagnose the lady at about 2 ticks), but the development has also been much steeper, causing the lady to experience almost all of the 7 main symptoms for the majority of the time. Hopefully, she got all better soon.
 =5. Conclusion=
-The main issue has, obviously, been data collection. As has been stated under Problem definition, the current sources are not only scarce, but also unreliable. However, I do believe that the positive side of my simulation is that it may be easily adjusted (symptoms added, thresholds edited, ''suspected-positivity-line'' moved, etc.) once we learn more about the disease. For now it may serve as a skeleton and, frankly, is quite as reliable for the purposes of self-diagnosis as many of the suspiciously expensive home-testing kits available online.
+The main issue has, obviously, been data collection. As has been stated under Problem definition, the current sources are not only scarce, but also unreliable. However, I do believe that the positive side of my simulation is that it may be easily adjusted (symptoms added, thresholds edited, ''suspected-positivity-line'' moved, etc.) once we learn more about the disease. For now it may serve as a skeleton and, frankly, may be quite as reliable for the purposes of self-diagnosis as many of the suspiciously expensive home-testing kits available online.
 =7. Code=
 =Sources=

@@ Line 64: / Line 64: @@
 =5. Conclusion=
 =7. Code=
 =Sources=

@@ Line 51: / Line 51: @@
 =4. Results=
-To demonstrate the use of this simulation, 3 specifically preset runs will be used to illustrate.
+To demonstrate the use of this simulation, 2 specifically preset runs will be used to illustrate.
-A. First, we have a young man coming to the simulation clinic. He has a ''Fever'' (1.0), a ''DryCough'' (0.6) and is experiencing some ''ShortnessOfBreath'' (0.5). He has no other symptoms. He is otherwise healthy, active and a non-smoker, therefore his ''contraction-susceptibility'' has been set to 0.0. If we gradually increase his ''exposure-to-virus'' over about 30 ticks, we can watch other symptoms develop at a steady rate. Around 12 ticks the man has been first diagnosed as suspected positive by the model.
+'''A.''' First, we have a young man coming to the simulation clinic. He has a ''Fever'' (1.0), a ''DryCough'' (0.6) and is experiencing some ''ShortnessOfBreath'' (0.5). He has no other symptoms. He is otherwise healthy, active and a non-smoker, therefore his ''contraction-susceptibility'' has been set to 0.0. If we gradually increase his ''exposure-to-virus'' over about 30 ticks, we can watch other symptoms develop at a steady rate. Around 12 ticks the man has been first diagnosed as suspected positive by the model.
 [[File:Stek15-results1.png]]
-B. Second, an elderly lady arrives at the clinic. She has recently been experiencing ''LossOfAppetite'' (1.0) and her ''BodyAches'' (0.8). Otherwise, she has no other symptoms. Due to her age and a smoking habit, her ''contraction-susceptibility'' has been set to 0.7. Let us gradually increase her ''exposure-to-virus'' over about 30 ticks to compare with the man from case A:
+'''B.''' Second, an elderly lady arrives at the clinic. She has recently been experiencing ''LossOfAppetite'' (1.0) and her ''BodyAches'' (0.8). Otherwise, she has no other symptoms. Due to her age and a smoking habit, her ''contraction-susceptibility'' has been set to 0.7. Let us gradually increase her ''exposure-to-virus'' over about 30 ticks to compare with the man from case A:
 [[File:Stek15-results2.png]]
-We can see that not only the symptoms developed much faster (we were already able to diagnose the lady at about 2 ticks), but the development has also been much steeper, causing the lady to experience almost all of the 7 main symptoms for the majority of the time. Hopefully she got all better soon.
+We can see that not only the symptoms developed much faster (we were already able to diagnose the lady at about 2 ticks), but the development has also been much steeper, causing the lady to experience almost all of the 7 main symptoms for the majority of the time. Hopefully, she got all better soon.
 =5. Conclusion=

← Older revision		Revision as of 12:58, 20 January 2021
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	=4. Results=		=4. Results=

		+	To demonstrate the use of this simulation, 3 specifically preset runs will be used to illustrate.

		+	A. First, we have a young man coming to the simulation clinic. He has a ''Fever'' (1.0), a ''DryCough'' (0.6) and is experiencing some ''ShortnessOfBreath'' (0.5). He has no other symptoms. He is otherwise healthy, active and a non-smoker, therefore his ''contraction-susceptibility'' has been set to 0.0. If we gradually increase his ''exposure-to-virus'' over about 30 ticks, we can watch other symptoms develop at a steady rate. Around 12 ticks the man has been first diagnosed as suspected positive by the model.
		+
		+	[[File:Stek15-results1.png]]
		+
		+	B. Second, an elderly lady arrives at the clinic. She has recently been experiencing ''LossOfAppetite'' (1.0) and her ''BodyAches'' (0.8). Otherwise, she has no other symptoms. Due to her age and a smoking habit, her ''contraction-susceptibility'' has been set to 0.7. Let us gradually increase her ''exposure-to-virus'' over about 30 ticks to compare with the man from case A:
		+
		+	[[File:Stek15-results2.png]]
		+
		+	We can see that not only the symptoms developed much faster (we were already able to diagnose the lady at about 2 ticks), but the development has also been much steeper, causing the lady to experience almost all of the 7 main symptoms for the majority of the time. Hopefully she got all better soon.

	=5. Conclusion=		=5. Conclusion=

@@ Line 47: / Line 47: @@
 '''a''' controls the steepness of the probability function and represents how much will a change in A affect the chance of activating the symptom. The parameter a has been adjusted according to the probability of a hospitalized COVID-19 patient developing the symptom.
-And finally, '''b''' represents the threshold of a symptom - the higher b, the more activity in the neighbors such symptom needs to become activated. To take in consideration false positivity, the parameter b has been adjusted according to the combined probabilities of a patient developing said symptom while sick with the COVID-19 virus, the common flu, or cold. For example, for a symptom with the probability of development of 0.90199, the threshold has been set to 0.09801. The more common a symptom is, the higher are the chances of it appearing alone, not being caused/followed by other symptoms.
+And finally, '''b''' represents the threshold of a symptom - the higher b, the more activity in the neighbors such symptom needs to become activated. To take in consideration false positivity, the parameter b has been adjusted according to the combined probabilities of a patient developing said symptom while sick with the COVID-19 virus, the common flu, or cold. For example, for a symptom with the probability of development of 0.90199, the threshold has been set to 0.09801. The more common a symptom is, the higher are the chances of it appearing on it's own (not being caused/followed by other symptoms).
 =4. Results=

@@ Line 16: / Line 16: @@
 The table below lists said symptoms, their percentual incidence in patients hospitalized with COVID-19, and the added probability '''P(A∪B∪C)''' of occurrence in any sick patient (considering COVID-19, the common cold, and the flu), calculated from data taken from https://www2.hse.ie/conditions/coronavirus/symptoms.html).
-. Fever ; 99% ; 99.1%
+[[File:Stek15-table1.png]]
 The use of these parameters in my simulation is explained in the following sections.

@@ Line 49: / Line 49: @@
 [[File:Stek15-model4.png]]
-With the sliders per symptom on the right side of the model, it is possible to intervene on a specific symptom by curing it (by lowering it to 0.0). Similarly, it is possible to first set up the network with several symptoms (of identical or differing values) and see how such a patient progresses in time.
+With the sliders per symptom on the right side of the model, it is possible to intervene on a specific symptom by curing it (by lowering it to 0.0). Similarly, it is possible to first set up the network with several symptoms (of identical or differing values) and see how such a patient progresses over time.
 [[File:Stek15-model3.png]]
-The probability come activated for each symptom is represented as '''1 / 1 + e^(a(b - A))'''.
+The probability of becoming activated for each symptom is represented as '''1 / 1 + e^(a(b - A))'''.
 Here, '''A''' represents the total amount of stress on a symptom (slider of symptom + ''exposure-to-virus'' + the activity of it's neighbors). In other words, A shows us how much pressure there is on the symptom to become activated.

@@ Line 37: / Line 37: @@
 =3. Model=
-This model is a representation of the COVID-19 virus, or rather of the effects said virus has on an ill person. Each node of the model represents one of the 7 symptoms listed above. The model simulates the development of said symptoms in a patient. If the symptom turns red, it became activated (experienced). Upon deactivation, it turns black again. Each symptom is connected to all the others in order to create a conclusive network.
+This model is a representation of the COVID-19 virus, or rather of the effects said virus has on an affected person. Each node of the model represents one of the 7 symptoms listed above. The model simulates the development of the symptoms in a patient. If the symptom turns red, it became activated (experienced). Upon deactivation, it turns black again. Each symptom is connected to all the others in order to create a conclusive network.
 [[File:Stek15-model1.png]]
@@ Line 57: / Line 57: @@
 Here, '''A''' represents the total amount of stress on a symptom (slider of symptom + ''exposure-to-virus'' + the activity of it's neighbors). In other words, A shows us how much pressure there is on the symptom to become activated.
-'''a''' controls the steepness of the probability function and represents how much will a change in A affect the chance of activating the symptom. The parameter a has been adjusted according to the probability of a hospitalized COVID-19 patient developing said symptom.
+'''a''' controls the steepness of the probability function and represents how much will a change in A affect the chance of activating the symptom. The parameter a has been adjusted according to the probability of a hospitalized COVID-19 patient developing the symptom.
 And finally, '''b''' represents the threshold of a symptom - the higher b, the more activity in the neighbors such symptom needs to become activated. To take in consideration false positivity, the parameter b has been adjusted according to the combined probabilities of a patient developing said symptom while sick with the COVID-19 virus, the common flu, or cold. For example, for a symptom with the probability of development of 0.90199, the threshold has been set to 0.09801. The more common a symptom is, the higher are the chances of it appearing alone, not being caused/followed by other symptoms.