CDMetaPOP-Disease Manuscript Figure Reproduction

Table of Contents

Introduction
Software Install
Recreation
Reproduction

Introduction

This repository contains the files to recreate and reproduce the figures and analyses in the manuscript:
Landguth, E. L., et al. (Submitted). "Simulating the Landscape Eco-Evolution of Host-Pathogen Systems with CDMetaPOP"

Full Authorship: Erin L. Landguth, Allison Williams, Marissa Roseman, Miracle Amadi, Baylor Fain, Marcel Kouete, Rhys A. Farrer, Amy J. Haeseler, Orly Razgour, Chris Richardson, Byron Weckworth, Julie Weckworth, Flora Whiting-Fawcett, Duncan Wilson, Casey C. Day

Software Install

To recreate the figures summary data is provided and all that needs to be done is to run the provided code. Figure 1, 2, and 3 use python and Figure 4, 5, and 6 use R.

Note

The provided codes should work with current releases of python and R packages, but environment setup is also provided.

To begin

Important

Clone this repo and use it as the working directory

Python environment

To setup the python environment make sure either Anaconda, Miniconda, or your favorite conda provider is installed. Then enter the following instructions in the terminal (please choose your favorite terminal: Anaconda prompt, Spyder terminal, bash, etc.):

conda create --name CDMetaPOP_Disease_env python
conda activate CDMetaPOP_Disease_env
pip install -r requirements.txt

R environment

To setup the R environment use Rstudio, double click the .Rprofile file (which will open Rstudio), and make sure Renv is installed (install.packages("renv")). Then enter the following instructions in the console:

renv::restore()

Recreation

Important

Follow the instructions in Software Install and begin each figure making process with this repo as your working directory

Python

To recreate Figure 1-3:

• Navigate to the desired directory within Figures, either Figure1, Figure2, or Figure3.
  • cd Figures/FigureX
• run
  • python Figure_X_from_data.py

The image for figure X (Figure_X.png) will be created in the figure_outputs directory within FigureX.

To recreate Table 3

• Navigate to Analysis
  • cd Figures/Analysis
• run
  • python Table_1_comparison_statistics.py

A file containing the tables values (Table_1_values.txt) will be created in Analysis.

R

To recreate Figure 4-6:

• Double click the .Rprofile file, which will open Rstudio
• Navigate to the desired directory within Figures, either Figure4, Figure5, or Figure6.
  • setwd("Figures/FigureX")
• run in the console
  • source("Figure_X_from_data.R")

The image for figure X (Figure_X.png) will be created in the figure_outputs directory with in FigureX.

Reproduction

Important

Follow the instructions in Software Install and begin each figure making process with this repo as your working directory

Note

CDMetaPOP v3.08 is provided in this repo, so CDMetaPOP does not have to be install again unless desired.

Figure 1

Note

~50 MB will be needed to store the data for this figure and each simulation wll take ~5 min.

To reproduce the data for figure 1, four cases must be simulated. The code to run each simulation is:

• SIR
  • python CDMetaPOP/CDMetaPOP.py Figures/Figure1/CDMetaPOP_inputs/SIR/ RunVars.csv output/output
• SEIR
  • python CDMetaPOP/CDMetaPOP.py Figures/Figure1/CDMetaPOP_inputs/SEIR/ RunVars.csv output/output
• SIRP
  • python CDMetaPOP/CDMetaPOP.py Figures/Figure1/CDMetaPOP_inputs/SIRP/ RunVars.csv output/output
• SIRS
  • python CDMetaPOP/CDMetaPOP.py Figures/Figure1/CDMetaPOP_inputs/SIRS/ RunVars.csv output/output

Once the simulations are completed:

• Rename each created directory to the corresponding model type
  • e.g. The directory that is created in Figures/Figure1/CDMetaPOP_inputs/SIR/output/ needs to be renamed to SIR
• Move the renamed folder to Figures/Figure1/Figure_1_from_source_data/

After all the data has been added to Figures/Figure1/Figure_1_from_source_data/.

• Navigate to Figure1.
  • cd Figures/Figure1
• run -python Figure_1_from_source.py

The image for figure 1 (Figure_1.png) will be created in the figure_outputs/from_source directory with in Figure1.

Figure 2

Note

~35 GB will be needed to store the data for this figure and the code will run for about ~60 hr.

To reproduce the data for figure 2 run:

• python Figure_2_from_source.py

The image for figure 1 (Figure_1.png) will be created in the figure_outputs/from_source directory with in Figure2.

Figure 3

Note

~35 GB will be needed to store the data for this figure and the code will run for about ~60 hr.

To reproduce the data for figure 3 run:

• python Figure_3_from_source.py

The image for figure 3 (Figure_3.png) will be created in the figure_outputs/from_source directory with in Figure3.

Figure 4

Note

~ 8 GB will be needed to store the data for this figure

To reproduce the data for figure 4 run:

• python CDMetaPOP/CDMetaPOP.py Figures/Figure4/CDMetaPOP_inputs/ RunVars.csv output/output

Once the simulation is completed:

• Rename the created directory to Aspatial_inputs.
  • e.g. The directory that is created in Figures/Figure4/CDMetaPOP_inputs/output/ needs to be renamed to Aspatial_inputs.
• Move the renamed folder to Figures/Figure4/Figure_4_from_source_data/

After the data has been added to Figures/Figure4/Figure_4_from_source_data/.

• Navigate to Figure4.
  • setwd("Figures/Figure4")
• run -source("Figure_4_from_source.R")

The image for figure 4 (Figure_4.png) will be created in the figure_outputs/from_source directory with in Figure4.

Figure 5 and 6

Note

~ 25 GB will be needed to store the data for this figure

Figure 5 and 6 use the same data. One can either run the simulation in Figure5 or Figure6 and then move the data to the other folder. These instructions will instruct the reader to create the simulations in Figure5 and the code for figure 6 will point to that data. To reproduce the data for figure 5 and 6 run:

• python CDMetaPOP/CDMetaPOP.py Figures/Figure5/CDMetaPOP_inputs/ RunVars.csv output/output

Once the simulation is completed:

• Rename the created directory to Spatial_inputs.
  • e.g. The directory that is created in either Figures/Figure5/CDMetaPOP_inputs/output/ needs to be renamed to Spatial_inputs.
• Move the renamed folder to Figures/Figure5/Figure_5_from_source_data/

After the data has been added to either Figures/Figure5/Figure_5_from_source_data/.

• For figure 5:

  • Navigate to the Figure5.
    • setwd("Figures/Figure5")
  • run -source("Figure_5_from_source.R")

  The image for figure 5 (Figure_5.png) will be created in the figure_outputs/from_source directory with in Figure5.

• For figure 6:

  • Navigate to the Figure6.
    • setwd("Figures/Figure6")
  • run -source("Figure_6_from_source.R")

  The image for figure 6 (Figure_6.png) will be created in the figure_outputs/from_source directory with in Figure6.