From 39cbbd188c10b7a81496af901e927976158c5fc9 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Sun, 21 Jul 2024 22:03:20 +0000 Subject: [PATCH] build based on 3b68a90 --- dev/.documenter-siteinfo.json | 2 +- dev/index.html | 4 +-- dev/license/index.html | 2 +- dev/news/index.html | 2 +- dev/objects.inv | 7 +++-- dev/package_development/index.html | 2 +- dev/reference/index.html | 2 +- dev/search_index.js | 2 +- dev/tutorial/04cadd6a.svg | 45 ++++++++++++++++++++++++++++++ dev/tutorial/c9ce82b6.svg | 45 ++++++++++++++++++++++++++++++ dev/tutorial/eb57c102.svg | 41 +++++++++++++++++++++++++++ dev/tutorial/index.html | 20 +++++++++++-- 12 files changed, 162 insertions(+), 12 deletions(-) create mode 100644 dev/tutorial/04cadd6a.svg create mode 100644 dev/tutorial/c9ce82b6.svg create mode 100644 dev/tutorial/eb57c102.svg diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 3917bb5..69a92e4 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-07-20T07:52:13","documenter_version":"1.5.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-07-21T22:03:17","documenter_version":"1.5.0"}} \ No newline at end of file diff --git a/dev/index.html b/dev/index.html index 53557b3..8c8d37e 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,3 +1,3 @@ -HOME · UCIWWEIHR.jl

UCIWWEIHR.jl

Welcome to the UCIWWEIHR.jl package documentation!

By : Christian O. Bernal Zelaya & Volodymyr M. Minin.

Introduction

UCIWWEIHR.jl is a Julia package for forecasting and nowcasting COVID-19 hospitalizations using pathogen genome concentrations. UCIWWEIHR.jl Package License

Features

  • Comprehensive library of Bayesian models
  • Simulation of infectious disease
  • Parameter estimation and model calibration
  • Sensitivity analysis and uncertainty quantification?
  • Visualization of results and MCMC evaluations(live?)

Installation

To install UCIWWEIHR.jl, you can use the Julia package manager. Open the Julia REPL and run the following command:

using Pkg
-Pkg.add("UCIWWEIHR")
+HOME · UCIWWEIHR.jl
GitHub

UCIWWEIHR.jl

Welcome to the UCIWWEIHR.jl package documentation!

By : Christian O. Bernal Zelaya & Volodymyr M. Minin.

Introduction

UCIWWEIHR.jl is a Julia package for forecasting and nowcasting COVID-19 hospitalizations using pathogen genome concentrations. UCIWWEIHR.jl Package License

Features

  • Comprehensive library of Bayesian models
  • Simulation of infectious disease
  • Parameter estimation and model calibration
  • Sensitivity analysis and uncertainty quantification?
  • Visualization of results and MCMC evaluations(live?)

Installation

To install UCIWWEIHR.jl, you can use the Julia package manager. Open the Julia REPL and run the following command:

using Pkg
+Pkg.add("UCIWWEIHR")
diff --git a/dev/license/index.html b/dev/license/index.html index 77d5d5c..5c0a2e2 100644 --- a/dev/license/index.html +++ b/dev/license/index.html @@ -1,2 +1,2 @@ -LICENSE · UCIWWEIHR.jl

UCIWWEIHR.jl Package License

The UCIWWEIHR.jl package is licensed under the MIT License.

MIT License

MIT License

Copyright (c) 2024 Christian O. Bernal Zelaya

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

+LICENSE · UCIWWEIHR.jl
GitHub

UCIWWEIHR.jl Package License

The UCIWWEIHR.jl package is licensed under the MIT License.

MIT License

MIT License

Copyright (c) 2024 Christian O. Bernal Zelaya

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

diff --git a/dev/news/index.html b/dev/news/index.html index 0ced15f..178f3bd 100644 --- a/dev/news/index.html +++ b/dev/news/index.html @@ -1,2 +1,2 @@ -NEWS · UCIWWEIHR.jl
+NEWS · UCIWWEIHR.jl
GitHub
diff --git a/dev/objects.inv b/dev/objects.inv index e3bb3de..5002b55 100644 --- a/dev/objects.inv +++ b/dev/objects.inv @@ -2,5 +2,8 @@ # Project: UCIWWEIHR.jl # Version: 1.0.0-DEV # The remainder of this file is compressed using zlib. -xTo0.fTUf4U(6YiLQHȖ Ewىn#p3 -LC3q_ )cfE21>FTf[Ha9>M쁹y(B|6c>,F$Dz:4ױ:+1uv]D -<9>{G]]F*m$kls_>5(q+waDߡ։J\@:Q汋iY&.sT6PC!@E|v30'N;mm>ZvTiE\(`wfy]%6kO(:St=?#&fa'Ez~ =ؘ9: ]k40h`1GmLw.( wXVy2wG`Z|9g*;Ex}<[O2n8FWʗ۔ o \ No newline at end of file +xUn@}WL5M)o\*D *ǩ5I[;6J {̙ٙY_r\نJ|TO6泻_*D0ƚ~p.n0"0?woln23#'P.70=FP5\ՆӷaL6u$d q>bA-ҳPe@ƨ:Ʒb_ +Ť;J?6nYW.Uml1;N͗S Dh#ToxØM"Eu\Z&(PP̅wk*!^,r[1)cv#bŃSDBBY6bjWlƘg|/u|TeZ&'QTU|-vFuOPkSldq cTWU2=V;yU-u,__:) 7v$\nx[w \ No newline at end of file diff --git a/dev/package_development/index.html b/dev/package_development/index.html index 4bf94c2..a644075 100644 --- a/dev/package_development/index.html +++ b/dev/package_development/index.html @@ -1,2 +1,2 @@ -PACKAGE DEVELOPMENT · UCIWWEIHR.jl

Package Development Updates

[Version X.X.X] - YYYY-MM-DD

Added

  • Feature 1: Description of the feature that was added.
  • Feature 2: Description of the feature that was added.

Changed

  • Change 1: Description of the change that was made.
  • Change 2: Description of the change that was made.

Deprecated

  • Deprecated feature 1: Description of the feature that was deprecated.
  • Deprecated feature 2: Description of the feature that was deprecated.

Removed

  • Removed feature 1: Description of the feature that was removed.
  • Removed feature 2: Description of the feature that was removed.

Fixed

  • Bug fix 1: Description of the bug that was fixed.
  • Bug fix 2: Description of the bug that was fixed.
+PACKAGE DEVELOPMENT · UCIWWEIHR.jl
GitHub

Package Development Updates

[Version X.X.X] - YYYY-MM-DD

Added

  • Feature 1: Description of the feature that was added.
  • Feature 2: Description of the feature that was added.

Changed

  • Change 1: Description of the change that was made.
  • Change 2: Description of the change that was made.

Deprecated

  • Deprecated feature 1: Description of the feature that was deprecated.
  • Deprecated feature 2: Description of the feature that was deprecated.

Removed

  • Removed feature 1: Description of the feature that was removed.
  • Removed feature 2: Description of the feature that was removed.

Fixed

  • Bug fix 1: Description of the bug that was fixed.
  • Bug fix 2: Description of the bug that was fixed.
diff --git a/dev/reference/index.html b/dev/reference/index.html index 930a3f6..797b923 100644 --- a/dev/reference/index.html +++ b/dev/reference/index.html @@ -1,2 +1,2 @@ -REFERENCE · UCIWWEIHR.jl
+REFERENCE · UCIWWEIHR.jl
GitHub

Reference

Contents

Index

UCIWWEIHR.NegativeBinomial2 — Method

Create a re-parametrized negative binomial distribution in terms of mean and overdispersion.

Arguments

  • μ: Mean of the distribution.
  • ϕ: Overdispersion parameter.

Returns

A Distributions.NegativeBinomial distribution object.

source
UCIWWEIHR.eihr_ode! — Method

eihr_ode!(du, u, p, t)

Calculate the ordinary differential equations (ODEs) for the EIHR model.

Parameters:

  • du: Array{Float64,1} - The derivative of the state variables.
  • u: Array{Float64,1} - The current state variables.
  • p: Tuple{Float64,Float64,Float64,Float64,Float64} - The model parameters (alpha, gamma, nu, w, epsilon).
  • t: Float64 - The current time.

Returns:

  • du: Array{Float64,1} - The derivative of the state variables.
source
UCIWWEIHR.generate_simulation_data_ww_eihr — Function

Generating Simulation Data for Wastewater EIHR

To generate simulation data for wastewater EIHR, you can use the generate_simulation_data_ww_eihr function defined in the UCIWWEIHR.jl package. This function allows you to customize various parameters for the simulation.

Function Signature

```julia

Arguments

  • time_points::Int64: Number of time points wanted for simulation. Default value is 150.
  • seed::Int64: Seed for random number generation. Default value is 1.
  • E_init::Int64: Initial number of exposed individuals. Default value is 200.
  • I_init::Int64: Initial number of infected individuals. Default value is 100.
  • H_init::Int64: Initial number of hospitalized individuals. Default value is 20.
  • gamma::Float64: Rate of incubation. Default value is 1/4.
  • nu::Float64: Rate of leaving the infected compartment. Default value is 1/7.
  • epsilon::Float64: Rate of hospitalization recovery. Default value is 1/5.
  • rho_gene::Float64: Contribution of infected individual's pathogen genome into wastewater. Default value is 0.011.
  • tau::Float64: Scale/variation of the log concentration of pathogen genome in wastewater. Default value is 0.1.
  • df::Float64: Degrees of freedom for generalized t distribution for log concentration of pathogen genome in wastewater. Default value is 29.
  • sigma_hosp::Float64: Standard deviation for the negative binomial distribution for hospital data. Default value is 800.
  • Rt_init::Float64: Initial value of the time-varying reproduction number. Default value is 1.
  • sigma_Rt::Float64: Standard deviation for random walk of time-varying reproduction number. Default value is sqrt(0.02).
  • w_init::Float64: Initial value of the time-varying hospitalization rate. Default value is 0.35.
  • sigma_w::Float64: Standard deviation for random walk of time-varying hospitalization rate. Default value is sqrt(0.02).
source
UCIWWEIHR.sum_values — Method
sum_values(x,y)

This is an example of Docstring. This function receives two numbers x and y and returns the sum of the squares.

\[x^1 + y^1 \]

source
diff --git a/dev/search_index.js b/dev/search_index.js index f4531de..8ca7bf8 100644 --- a/dev/search_index.js +++ b/dev/search_index.js @@ -1,3 +1,3 @@ var documenterSearchIndex = {"docs": -[{"location":"license/#license","page":"LICENSE","title":"UCIWWEIHR.jl Package License","text":"","category":"section"},{"location":"license/","page":"LICENSE","title":"LICENSE","text":"The UCIWWEIHR.jl package is licensed under the MIT License.","category":"page"},{"location":"license/#MIT-License","page":"LICENSE","title":"MIT License","text":"","category":"section"},{"location":"license/","page":"LICENSE","title":"LICENSE","text":"MIT License","category":"page"},{"location":"license/","page":"LICENSE","title":"LICENSE","text":"Copyright (c) 2024 Christian O. Bernal Zelaya","category":"page"},{"location":"license/","page":"LICENSE","title":"LICENSE","text":"Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:","category":"page"},{"location":"license/","page":"LICENSE","title":"LICENSE","text":"The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.","category":"page"},{"location":"license/","page":"LICENSE","title":"LICENSE","text":"THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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Concentration of Pathogen Genome in WW","text":"","category":"section"},{"location":"tutorial/","page":"TUTORIAL","title":"TUTORIAL","text":"plot(df.obstimes, df.log_ww_conc,\n label=nothing,\n xlabel=\"Obstimes\", \n ylabel=\"Conc. of Pathogen Genome in WW\", \n title=\"Plot of Conc. of Pathogen Genome in WW Over Time\")","category":"page"},{"location":"tutorial/#2.2.-Hospitalizations","page":"TUTORIAL","title":"2.2. Hospitalizations","text":"","category":"section"},{"location":"tutorial/","page":"TUTORIAL","title":"TUTORIAL","text":"plot(df.obstimes, df.hosp, \n label=nothing,\n xlabel=\"Obstimes\", \n ylabel=\"Hosp\", \n title=\"Plot of Hosp Over Time\")","category":"page"},{"location":"tutorial/#2.3.-Reproductive-Number","page":"TUTORIAL","title":"2.3. Reproductive Number","text":"","category":"section"},{"location":"tutorial/","page":"TUTORIAL","title":"TUTORIAL","text":"plot(df.obstimes, df.rt, \n label=nothing,\n xlabel=\"Obstimes\", \n ylabel=\"RT\", \n title=\"Plot of RT Over Time\")","category":"page"},{"location":"package_development/#package-development-updates","page":"PACKAGE DEVELOPMENT","title":"Package Development Updates","text":"","category":"section"},{"location":"package_development/#[Version-X.X.X]-YYYY-MM-DD","page":"PACKAGE DEVELOPMENT","title":"[Version X.X.X] - YYYY-MM-DD","text":"","category":"section"},{"location":"package_development/#Added","page":"PACKAGE DEVELOPMENT","title":"Added","text":"","category":"section"},{"location":"package_development/","page":"PACKAGE DEVELOPMENT","title":"PACKAGE DEVELOPMENT","text":"Feature 1: Description of the feature that was added.\nFeature 2: Description of the feature that was added.","category":"page"},{"location":"package_development/#Changed","page":"PACKAGE DEVELOPMENT","title":"Changed","text":"","category":"section"},{"location":"package_development/","page":"PACKAGE DEVELOPMENT","title":"PACKAGE DEVELOPMENT","text":"Change 1: Description of the change that was made.\nChange 2: Description of the change that was made.","category":"page"},{"location":"package_development/#Deprecated","page":"PACKAGE DEVELOPMENT","title":"Deprecated","text":"","category":"section"},{"location":"package_development/","page":"PACKAGE DEVELOPMENT","title":"PACKAGE DEVELOPMENT","text":"Deprecated feature 1: Description of the feature that was deprecated.\nDeprecated feature 2: Description of the feature that was deprecated.","category":"page"},{"location":"package_development/#Removed","page":"PACKAGE DEVELOPMENT","title":"Removed","text":"","category":"section"},{"location":"package_development/","page":"PACKAGE DEVELOPMENT","title":"PACKAGE DEVELOPMENT","text":"Removed feature 1: Description of the feature that was removed.\nRemoved feature 2: Description of the feature that was removed.","category":"page"},{"location":"package_development/#Fixed","page":"PACKAGE DEVELOPMENT","title":"Fixed","text":"","category":"section"},{"location":"package_development/","page":"PACKAGE DEVELOPMENT","title":"PACKAGE DEVELOPMENT","text":"Bug fix 1: Description of the bug that was fixed.\nBug fix 2: Description of the bug that was fixed.","category":"page"}] } diff --git a/dev/tutorial/04cadd6a.svg b/dev/tutorial/04cadd6a.svg new file mode 100644 index 0000000..e724730 --- /dev/null +++ b/dev/tutorial/04cadd6a.svg @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dev/tutorial/c9ce82b6.svg b/dev/tutorial/c9ce82b6.svg new file mode 100644 index 0000000..7cc61cc --- /dev/null +++ b/dev/tutorial/c9ce82b6.svg @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dev/tutorial/eb57c102.svg b/dev/tutorial/eb57c102.svg new file mode 100644 index 0000000..3cf0685 --- /dev/null +++ b/dev/tutorial/eb57c102.svg @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dev/tutorial/index.html b/dev/tutorial/index.html index 9a15dda..5b2d449 100644 --- a/dev/tutorial/index.html +++ b/dev/tutorial/index.html @@ -1,3 +1,19 @@ -TUTORIAL · UCIWWEIHR.jl

Tutorials

Welcome to the Tutorials page for the UCIWWEIHR.jl project. This section provides step-by-step guides and examples to help you get started with using the package and understanding its features.

Getting Started

Installation

To install the UCIWWEIHR.jl package, open the Julia REPL and run the following command:

using Pkg
-Pkg.add("UCIWWEIHR")
+TUTORIAL · UCIWWEIHR.jl
GitHub

Tutorials

Welcome to the Tutorials page for the UCIWWEIHR.jl project. This section provides step-by-step guides and examples to help you get started with using the package and understanding its features.

1. Getting Started

1.1 Installation

To install the UCIWWEIHR.jl package, open the Julia REPL and run the following command:

using Pkg
+Pkg.add("UCIWWEIHR")

2. Generating simulated data

This package provides a way to also simulate data using the model specified in the future paper. The function called generate_simulation_data_ww_eihr can be used to generate synthetic data for a given number of samples and features. Here we provide a way to generate synthetic data for the default settings of generate_simulation_data_ww_eihr:

using UCIWWEIHR
+using Plots
+# Running simulation function with defaults
+df = generate_simulation_data_ww_eihr()
+first(df, 5)
5×4 DataFrame
Rowobstimeslog_ww_conchosprt
Int64Float64Float64Float64
110.49360226.00.99777
220.71674323.00.972634
330.58837733.01.00913
440.96313739.01.06655
550.55022828.01.03195

Here we can make simple plots to visualize the data generated using the Plots.jl package.

2.1. Concentration of Pathogen Genome in WW

plot(df.obstimes, df.log_ww_conc,
+    label=nothing,
+    xlabel="Obstimes",
+    ylabel="Conc. of Pathogen Genome in WW",
+    title="Plot of Conc. of Pathogen Genome in WW Over Time")
Example block output

2.2. Hospitalizations

plot(df.obstimes, df.hosp,
+    label=nothing,
+    xlabel="Obstimes",
+    ylabel="Hosp",
+    title="Plot of Hosp Over Time")
Example block output

2.3. Reproductive Number

plot(df.obstimes, df.rt,
+    label=nothing,
+    xlabel="Obstimes",
+    ylabel="RT",
+    title="Plot of RT Over Time")
Example block output