SIR Model in Mathematical Epidemiology using Python Jupyter Notebook

SIR Model in Mathematical Epidemiology using Python Jupyter Notebook

SIR Model in Mathematical Epidemiology using Python Jupyter Notebook

my channel so today i’m going to explain about how to use the jupiter notebook in order to make the sir model sir model stand for data online please continue to subscribe like and share all our videos we provide a very comprehensive online process free of charge long-term video coming together.

#spss #kajidataonline #epiinfo #ppkp #ministryofhealth #ilkkm **

Dataset Google Sheet: CLICK HERE

**Dataset/ Script Jupyter: CLICK HERE

Part II of this video: CLICK HERE

susceptible infection and recovery model so the first of all we open the anaconda and after that the anaconda are going to open you this jupiter notebook interface and then i’m going to use the phyton 3.8.0 so uh this is my anaconda version so let us type the code and then we are going to run the analysis together so the first of all um we begin with the code type here as import import packages so we need to import the scripting into grid and then we also import numpy okay numpy okay this is wrong import and then we are also going to import the met plot library pi plot as plt okay this is the first one and then the second onewe are going to make the ordinal ode ode means that differential equation we are going to make sir underscore model and then we are going to run for y beta gamma and then we are going to specify our model s i r is equal to I and then we are going to make the differential equation ds underscore dt uh beta times by s times by I then d i underscore dt it’s equal to beta times by s times by i minus gamma times my I and then the r and let’s call dt the rate of change for this group gamma times by i and then we are going to specify a return in bracket semicolon d s underscore dd comma d i underscore dt comma and then the last one at least is dr underscored so this is the second instructions that we need to specify under the jupiter notebookso the next one we are going to set the initial condition  so initial condition is very important in sir model when you specify the s0 so in this case uh i’m going to specify it using the conditions that related to our data set here  so the initial condition is already set at this level for example okay 0.009 is actually a proportion  uh taken from a specific study and then we’re going to specify it under here and then our infection io is infection also beingspecified under this numerical expression and then we can also specify the r and all these data can be download or can be copied accordingly if you want it inside the link provided okay so we are going to specify the time vector so the time vector is actually t it’s equal to numpy in space this is the condition where we specify the graphical measure so i’m going to use 200 1000 so you just make it much more bigger a little bit and then we specify for the result okay for the result we are going to use the solution it’s equal to script by i’m sorry skip i dot in the grid dot audience sr underscore model and then we specify this one as a record colon initial condition i o r o and then t a r g s okay and then we specify for the beta and also gamma all right so the next one the last word numpy dot array and then we are going to say solution all right so this is where we are setting up our integrated sir model according to the initial condition so this is the example of the initial condition they already been set using this data so this data is basically how many people is already infected here and then how many people is already being recovered in terms of proportionate values okay so the next one we need to add the last but not least is actually plotting the result this is the most important part of any sir plt dot figure so in this i’m going to specify the fixed size is equal to in bracket 10 6 10 8 was okay then six also can alright so the next one is plt dot plot i’m going to plot it according to the t solution for the specific condition graph or double dot comon space by zero and

Susceptible Infection Recovery (SIR) Model in Mathematical Epidemiology using Python and Google Sheet Beta Gamma

then i’m going to label this one so i’m going to instruct the computer to label this one as s before that in bracket and don’t forget about that as in bracket so this is meant uh susceptible okay uh same also actually you can just copy all this thing for the next one copy and paste copy and paste but you must change the number one two and three because it is indicate the levels of uh these item and then this one is correspond to the i and then this one is correspond for the r then you are going to tell the computer to make the plot dot grid so that it can give you some grid to help you identify the condition legend also and then plt dot x level we’re going to label it as time so usually we specify this time as days and then plt dot y level so as you know the y level in my case is actually a proportion of power proportions of the data they’ve been getting from a total population and then pld title titles okay don’t forget to put the sir model and then plt dot show okay so after this we can run our data but um I want to give you the idea here is actually not finished because we don’t specify our beta and gamma therefore you need to specify what is your beta and then what is your gamma so this follow is actually here okay this is correspond to the beta and then another one is correspond to the gamma this is the average beta and gamma okay if you want to know how to calculate that one i i’m going to share the link for this uh spreadsheet to you and then you can run it by also i’m just going to share with you um you have to save your file so in this case i’ve already saved my file in the sir model name so i’m going to run it so after you run it and then the conditions of the plot are going to be produced until this so this is the example of the sir model that already been indicated by the system uh it’s showing to you that basically the infection will start around this value and then the proportions are going to be the key and then the recovered personnel are going to be increase over the time so if you want to change accordingly uh your beta and gamma and then also your proportion for the initial conditions of the susceptible infected and also recovery you can do it automatically in this module so um that’s all for my presentation about sir model  hope that this one are going to help you a lot in terms of making a prediction so let us discuss and if you think that this model is good or you need more explanation please let me know in the comment below so if you want to have these uh codes you can just download the links in the description and if you want also the google sheet indicate the condition of the data that already being specified to the sir model and you can download it in the description below also so that’s all ladies and gentlemen see you again until the next time don’t forget to like subscribe and share thank you

 

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