HPC sh scripts

Building Networks

create_network_farm.sh

This script runs 'create_network_farm.r'

Input

It gets two arguments:

1. The number of the experiment to analyze (the id of set of abundance data from which to build the co-occurrance network).
2. The name of the farm to build the network for.

create_all_networks.sh

This script queues the script 'create_network_farm.sh' to be run as a job on the HPC, once for each farm.

Input

1. The number of the experiment to analyze (the id of set of abundance data from which to build the co-occurrance network).

run_shuffled_farm.sh

This script makes a folder and prepares it and then queues 'create_network_farm.sh' for each farm to run on this folder. It does that for each shuffled data (IDs 1-100).

run_shuffled_farm_500.sh

This script makes a folder and prepares it and then queues 'create_network_farm.sh' for each farm to run on this folder. It does that for each shuffled data (IDs 1-500).

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Network Modularity Analysis

modularity_analysis_shuffled_farm.sh

This script runs 'modularity_analysis_shuffled_farm.R'

Input

1. The number of the experiment to analyze - the id of multilayer network to run Infomap on.

modularity_analysis_pf_shuffled.sh

This script runs 'modularity_analysis_pf_shuffled.R'

modularity_analysis_pf_shuffled_500.sh

This script uses the experiment folder (made by 'run_shuffled_farm.sh'), prepares it and then queues 'modularity_analysis_pf_shuffled.sh' to run on this folder. It does that for each shuffled network (IDs 1-500).

Partner Fidelity Analysis

shuffled_partner_fidelity.sh

This script runs 'shuffled_partner_fidelity.R'

Input

1. The number of the experiment to analyze - the id of network to check partner fidelity for.

shuffled_partner_fidelity_500.sh

This script uses the experiment folder (made by 'run_shuffled_farm.sh'), prepares it and then queues 'modularity_analysis_pf_shuffled.sh' to run on this folder. It does that for each shuffled network (IDs 1-500).