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MITCOVID2.jl
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### A Pluto.jl notebook ###
# v0.17.4
using Markdown
using InteractiveUtils
# ╔═╡ c6246074-6ee3-11ec-0279-23f36ba7bb51
using Pkg
# ╔═╡ 161039a4-9da6-4339-8a18-d98e20fe3d20
using Interact
# ╔═╡ b07f6111-9897-4589-8c88-98fa55c02e75
using CSV
# ╔═╡ 99e6b1f9-0b37-475e-ba7d-d5c52fe9c776
using DataFrames
# ╔═╡ a2be8c66-f666-4683-b425-d598003c1188
using WebIO
# ╔═╡ 8698b51c-c5f3-4f8a-a7fb-c5043c8eabeb
using Plots
# ╔═╡ fec5714a-40cd-4de2-87c3-9d16bea6f2e1
using Dates
# ╔═╡ c624604c-6ee3-11ec-2a15-bbe6fcffde98
html"""
<div>Happy holiday! Remember to take care of yourself and your loved ones!</div>
<div id="snow"></div>
<style>
body:not(.disable_ui):not(.more-specificity) {
background-color:#e9ecff;
}
pluto-output{
border-radius: 0px 8px 0px 0px;
background-color:#e9ecff;
}
#snow {
position: fixed;
top: 0;
left: 0;
right: 0;
bottom: 0;
pointer-events: none;
z-index: 1000;
}
</style>
<script src="https://cdn.jsdelivr.net/particles.js/2.0.0/particles.min.js"></script>
<script>
setTimeout(() => window.particlesJS("snow", {
"particles": {
"number": {
"value": 70,
"density": {
"enable": true,
"value_area": 800
}
},
"color": {
"value": "#ffffff"
},
"opacity": {
"value": 0.7,
"random": false,
"anim": {
"enable": false
}
},
"size": {
"value": 5,
"random": true,
"anim": {
"enable": false
}
},
"line_linked": {
"enable": false
},
"move": {
"enable": true,
"speed": 5,
"direction": "bottom",
"random": true,
"straight": false,
"out_mode": "out",
"bounce": false,
"attract": {
"enable": true,
"rotateX": 300,
"rotateY": 1200
}
}
},
"interactivity": {
"events": {
"onhover": {
"enable": false
},
"onclick": {
"enable": false
},
"resize": false
}
},
"retina_detect": true
}), 3000);
</script>
"""
# ╔═╡ 9ec943f6-80e5-4432-ab9c-4ed07d2edf8d
url ="https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
# ╔═╡ 473d0971-00d6-4b9b-8a5e-6ad29031e0ee
download(url, "covid_data.csv")
# ╔═╡ 96c190fc-191b-4c78-ac07-e9a80bc36534
CSV.read("covid_data.csv", DataFrame)
# ╔═╡ 58178f67-6c78-42c0-8b69-e0c69abcad4c
data = CSV.read("covid_data.csv", DataFrame);
# ╔═╡ 46d524f6-c982-4fff-b08d-548a22b83c29
data
# ╔═╡ c6b7e0d6-6d5c-40bf-ace1-dc0b6b2886b7
countries = collect(data[:,2])
# ╔═╡ 7b8d012a-a96a-497a-ac53-498b5d7170b4
unique_countries = unique(countries)
# ╔═╡ f22021a8-6049-4fd8-a8cc-2dd901633f49
startswith("I")
# ╔═╡ add27458-66d4-4e14-ada0-21a84e4a5117
I_countries = [startswith(country,"I") for country in countries];
# ╔═╡ 31353f8c-fbcd-4eda-8628-faeea9c9135a
data[I_countries, :]
# ╔═╡ 0aa83a4f-bfa5-4ed4-a855-fc87c3f49620
countries .== "India"
# ╔═╡ 52bdb813-f51f-4b9f-94a5-6512313c059a
IND_row = findfirst(countries .=="India")
# ╔═╡ 6276d8b2-1d80-445e-b9fd-ce41108a2e1f
IND_data_row = data[IND_row, :]
# ╔═╡ 03a08a0a-d924-4eef-87a3-93b2b91bcec7
IND_data = collect(IND_data_row[5:end])
# ╔═╡ c94ecc1a-0bd0-42bd-b179-64afb4f1a6c9
plot(IND_data);
# ╔═╡ 91bfd14c-3766-49b4-ac37-24a5a45ea940
date_strings = String.(names(data))[5:end]
# ╔═╡ a2a8b9c2-f86a-4532-bcdc-2501b2a855ef
format = Dates.DateFormat("m/d/Y")
# ╔═╡ 4f756d10-ee41-420f-bd71-435a0e5856f2
dates = parse.(Date, date_strings, format) + Year(2000);
# ╔═╡ 037105b4-7bad-4641-b180-21c4eae3c184
plot(dates,IND_data, xticks=dates[1:60:end], xrotation=45, leg=:topleft, label="India COVID-19 Cases");
# ╔═╡ 9299543d-a043-4b10-b77e-1b60aebbe428
xlabel!("Date");
# ╔═╡ c88fe033-428c-4924-8d32-7b68d9d3a1ea
ylabel!("India Confirmed Cases")
# ╔═╡ 0c575356-9b02-4544-b9d4-2adb74785116
``I_{n+1} = I_n + (cI_n)``
# ╔═╡ fada77cc-8d79-46c0-a618-bb02d006be0f
I0 = 1
# ╔═╡ 9586acfa-accb-4ec8-8c11-8b3e36a97c01
I_0 = 1
# ╔═╡ 3c796505-f698-4ad8-bd17-f202e326eb56
I₀ = 1
# ╔═╡ fa2b70c3-b40b-4787-bb62-5c3cf0bb2125
c = 0.01 # average no. of people that each individual infects on each day
# ╔═╡ 26e1a780-7559-43b4-8e1f-3329b537f26f
λ = 1 + c ;
# ╔═╡ dca94f80-4f30-4339-9d9d-343607fcac83
I_1 = λ * I_0
# ╔═╡ 2c04f0d0-54a3-490f-8611-91f9a723205c
I_2 = λ * I_1
# ╔═╡ ea0098e0-93b2-49f9-a228-8ba1065607c0
I_3 = λ * I_2
# ╔═╡ 349ba73c-b638-4097-83dc-30f5cb92f59e
T=20
# ╔═╡ 261b66b3-46ff-4854-b7ce-83c05a59dadc
I = zeros(T)
# ╔═╡ a929e0c6-9935-4f59-9091-e0ce658abdfd
I[1] = I_0
# ╔═╡ 47facd64-1f46-457f-960c-8ca42792a52c
for n in 1:T-1
I[n+1] = λ * I[n]
@show n, I[n]
end
# ╔═╡ f5c8696a-b515-44aa-947d-d344e77cb9f2
I
# ╔═╡ ad049c2a-88ec-471e-bb7a-0f04fddd2e62
plot(I, m=:o, label="I[n]", legend=:topleft);
# ╔═╡ 35a78396-209e-41b4-8eeb-5fb22f1b163d
p = 0.02
# ╔═╡ 8a3537a2-8245-4428-8a83-f9385c9a5386
α = 0.01
# ╔═╡ 1951c463-59cc-43ea-ac4b-f4baf7cfbed3
N = 1000
# ╔═╡ afef1536-fd7e-47cc-8b6b-a9d4e716f882
function run_infection(T=20)
I = zeros(T)
I[1] = I_0
for n in 1:T-1
I[n+1] = λ * I[n]
end
return I
end
# ╔═╡ 9619a8e6-a1fd-4c27-9316-dd88c0a8c020
methods(run_infection)
# ╔═╡ fbecebf9-fc52-450a-8a4a-dd3d36c930e4
run_infection(10)
# ╔═╡ c962e3c2-a620-4fb5-8263-9e50066371e0
I_result1 = run_infection(10);
# ╔═╡ 9261c9aa-9101-43d8-8b5f-008191bd6965
end_T = 1000
# ╔═╡ d5e31593-ee2b-4d73-a7ff-06e5d7f2f691
plot(run_infection(1000),label="Exponential Infection Growth")
# ╔═╡ 612159b5-4cbb-4132-9e4d-7c8b712622e5
plot(run_infection(1000), yscale=:log10, label="Logarithmic Scale")
# ╔═╡ 54c37296-1fae-447b-a8fd-a792b60d2a57
I_result = run_infection(1000)
# ╔═╡ f56f1910-33c5-4ebe-8e0e-332752b8b923
I_result
# ╔═╡ d33b9f8b-9ffd-4f3f-809e-4cfdf6056d85
plot(I_result, m=:o)
# ╔═╡ 7c168d73-e3ec-4be0-9a37-d02e7afd98c7
plot(log10.(I_result))
# ╔═╡ 47990471-4301-427a-bf8a-d95e4c133b8d
ylabel!("log(I_n)")
# ╔═╡ 03ed1990-becf-4d5e-8082-b1649540b219
β(I, S) = p * α * S
# ╔═╡ 23d08bb2-a2dc-4d14-a787-c6c2997bf61b
I_20 = run_infection(20)
# ╔═╡ a559ae0b-468d-46d4-8e08-62f207ef4aa2
plot(I_20, m=:o)
# ╔═╡ bab09c8c-9d09-463f-bf2e-dd894402176a
plot(I_20, m=:o, yscale=:log10, label="Logarithmic Scale")
# ╔═╡ 23c0f7fd-facf-49e9-a4fb-c4186123a5bb
I_100= run_infection(100)
# ╔═╡ 77365d86-f39d-47ff-809e-6b7a8fc8f6f5
plot(I_100, yscale=:log10)
# ╔═╡ 390a3a67-7d80-42ea-a0e3-a29743e58dd5
c_average = 1.1
# ╔═╡ 0ce1fe85-7e68-4f61-bc22-b5c34e04f5ba
cs = [c_average + 0.1*randn() for i in 1:100]
# ╔═╡ 570b788b-1195-44a7-97c1-f2fe2c6ba828
scatter(cs)
# ╔═╡ 00000000-0000-0000-0000-000000000001
PLUTO_PROJECT_TOML_CONTENTS = """
[deps]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
Interact = "c601a237-2ae4-5e1e-952c-7a85b0c7eef1"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
WebIO = "0f1e0344-ec1d-5b48-a673-e5cf874b6c29"
[compat]
CSV = "~0.9.11"
DataFrames = "~1.3.1"
Interact = "~0.10.4"
Plots = "~1.25.4"
WebIO = "~0.8.16"
"""
# ╔═╡ 00000000-0000-0000-0000-000000000002
PLUTO_MANIFEST_TOML_CONTENTS = """
# This file is machine-generated - editing it directly is not advised
julia_version = "1.7.0"
manifest_format = "2.0"
[[deps.Adapt]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "9faf218ea18c51fcccaf956c8d39614c9d30fe8b"
uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
version = "3.3.2"
[[deps.ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
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uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
[[deps.AssetRegistry]]
deps = ["Distributed", "JSON", "Pidfile", "SHA", "Test"]
git-tree-sha1 = "b25e88db7944f98789130d7b503276bc34bc098e"
uuid = "bf4720bc-e11a-5d0c-854e-bdca1663c893"
version = "0.1.0"
[[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
[[deps.Bzip2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2"
uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
version = "1.0.8+0"
[[deps.CSSUtil]]
deps = ["Colors", "JSON", "Markdown", "Measures", "WebIO"]
git-tree-sha1 = "b9fb4b464ec10e860abe251b91d4d049934f7399"
uuid = "70588ee8-6100-5070-97c1-3cb50ed05fe8"
version = "0.1.1"
[[deps.CSV]]
deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"]
git-tree-sha1 = "49f14b6c56a2da47608fe30aed711b5882264d7a"
uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
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