netclop 0.8.1

Network clustering operations for geophysical fluid transport

Network clustering operations

Network clustering operations (netclop) is a command line interface for geophysical fluid transport network construction and associated clustering operations (e.g., community detection, significance clustering).

Installation

Use pipx to install and run in an isolated environment.

brew install pipx
pipx ensurepath

To install:

pipx install netclop

To upgrade:

pipx upgrade netclop

Use

Particle trajectories must be decomposed into initial and final latitude and longitude coordinates and stored in a positions file in the form initial_latitude,initial_longitude,final_latitude,final_longitude. Positions are binned with H3. Community detection uses Infomap.

netclop [GLOBAL OPTIONS] COMMAND [ARGS] [OPTIONS]

Global options

• --config CONFIG_PATH Path to a custom configuration YAML file

Commands

Partition

Constructs and partitions a network from positions, optionally demarcating significant assignments from statistical noise.

netclop partition POSITIONS_PATH [OPTIONS]

Arguments

• POSITIONS_PATH Path to the positions file.

Options

• --output, -o Path to the output file where the node list will be written.
• --significance-cluster, -sc Perform significance clustering to delineate noise
• --res Specifies the H3 grid resolution (range 0-15) used for domain discretization.
• --markov-time, -mt Tuning parameter of the spatial scale of detected structure."
• --variable-markov-time/--static-markov-time Allows for dynamic adjustment of Markov time with varying network density.

Plot

Plots a node list.

netclop plot NODE_PATH [OPTIONS]

Arguments

• NODE_PATH Path to a node list. Node names must be integer H3 indices.

Options

• --delineate-noise, -dn Delineates noise in plot if "significant" column flag in node list file