docker.md

In hannahschrenk/QtAC: Quantifying the Adaptive Cycle

Docker installation for running the QtAC container (optional)

Docker installation in Debian based distributions (Ubuntu):

$ sudo apt update

$ sudo apt install ca-certificates curl gnupg lsb-release

$ curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o \
     /usr/share/keyrings/docker-archive-keyring.gpg
$ echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] \
     https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

$ sudo apt-get update

$ sudo apt-get install docker-ce docker-ce-cli containerd.io

Docker installation in Windows 10: To install Docker in Windows 10 follow the steps here

Docker installation in macOS: To install Docker in macOS follow the steps here

Test Docker installation: Run this example in a terminal to make sure Docker is installed correctly: docker run hello-world

NOTE In linux you have to add sudo before docker!

Run QtAC container and example

Linux (Ubuntu):

• Download one time the image from Docker Hub. In a terminal copy and paste the following line: docker pull hannahschrenk/qtac:latest

• Run the container: The downloaded image contains a example dataset to test the features of the package.

sudo docker run -it -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix \
                                     --user="$(id --user):$(id --group)" \
                                     --device=/dev/dri:/dev/dri \
                                     -v $PWD:/output/ hannahschrenk/qtac:latest

The container will pop an R terminal where we can start using the QtAC package.

NOTE: $PWD is the current directory in the terminal (linux/macOS).

Windows 10/11:

• Download one time the image from Docker Hub. In a terminal copy and paste the following line: docker pull hannahschrenk/qtac:latest

macOS (XX.XX):

• Download one time the image from Docker Hub. In a terminal copy and paste the following line: docker pull hannahschrenk/qtac:latest

Copy and paste.

1. INITIALIZATION:

library(QtAC)

work_folder  <- "/output/"                  # internal folder in the container mounted on $PWD
observ_data  <- "/Example/QtAC_SIHUMI.txt"  # internal file containing the example data in the container
infodyn_path <- "/dist/MTinfodynamics.jar"  # internal path of the MTinfodynamics.jar file in the container
setwd(work_folder)

num_timepoints <- 30   # length of the time windows serving as basis for the transfer entropy calculations
signfac <- 0.1         # significance level

1. CALCULATIONS:

# load the data
Data <- QtAC.TXT.reader(observ_data, col_names = FALSE, row_names = TRUE)

# compute networks of information transfer for every time point starting from num_timepoints
result_mtx <- QtAC(Data, num_timepoints, infodyn_path, l = 10L, k = 10L, delay = 2L)

# take only information transfers passing the significance level into account
result_mtx_sig <- QtAC.signfactor(result_mtx, signfac)

# calculate the three systemic variables for every network
maturation <- QtAC.maturation(result_mtx_sig)

1. VISUALIZATIONS:

# plot the first network of information transfers (corresponding to time point 30) and save it
QtAC.network(result_mtx_sig, num_mtx = 1, edge_label = TRUE, arrow_width = 2, layout = "nicely", save = TRUE)

# plot the development of potential, connectedness, and resilience over time and save it
QtAC.2dplot(maturation, save = TRUE)

# plot the development of potential and connectedness w.r.t. each other and save it
QtAC.2dmixplot(maturation, "potential", "connectedness", save = TRUE)

# plot a 3D plot of potential, connectedness, and resilience
QtAC.3dplot(maturation, mat_points = TRUE)

NOTE: All image files are saved in the current directory in the terminal.

1. EXIT CONTAINER:

quit()

hannahschrenk/QtAC documentation built on July 27, 2023, 5:35 a.m.