Table of Contents

move2 (Movebank)

These instructions describe how to use the R package move2 on the HPC cluster:

Using move2 on interactive sessions

On this system, credentials are stored per R session using the keyring env backend (expected behaviour on headless nodes).

0. Start an interactive session

~$ srun -p ceab --pty bash

1. Load the R module

~$ module load R-bundle-CRAN

Start R, 

~$ R

2. Check if move2 is installed (install if needed)

Check whether move2 is installed: 

> library(move2)

If not installed (typical on HPCs), install it in your user library: 

> install.packages("move2", repos = "https://cloud.r-project.org")

The package will be installed under ~/R/x86_64-pc-linux-gnu-library/.

3. Load package and store Movebank credentials

> library(move2)

> movebank_store_credentials(<movebank_user_name>)

You will be prompted once for your Movebank password. Credentials remain valid only for the current R session.

A warning about the env backend may appear. This is expected on this system.

4. Check available studies

List all accessible studies: 

> movebank_download_study_info()

List only studies with download access: 

> movebank_download_study_info(i_have_download_access = TRUE)

Query a specific study by ID: 

> movebank_download_study_info(id = 2911040)

5. Suppress backend warning messages (optional)

To avoid repeated warnings about the keyring backend: 

suppressWarnings(
  movebank_download_study_info()
)

This does not affect functionality.

6. Download tracking data from a study

Resolve the study ID if you just know the name: 

suppressWarnings(
  study_id <- movebank_get_study_id(
    study_id = "Galapagos Albatrosses"
  )
)

Then download data with filters: 

suppressWarnings(
  data <- movebank_download_study(
    study_id,
    sensor_type_id = "gps",
    timestamp_start = as.POSIXct("2008-08-01 00:00:00"),
    timestamp_end   = as.POSIXct("2008-08-02 00:00:00")
  )
)

data is returned as a move2 object and can be processed directly with the package’s tools.

7.Notes and limitations

Using move2 on Slurm batch jobs

Because the system is headless, Movebank credentials must be provided via environment variables (lost on shell session exit).

NEVER hard-code passwords in your R scripts !!

1. Prepare Movebank credentials

Before submitting the job, export your credentials in the shell. 

export MOVEBANK_USER="your_movebank_user_name"
export MOVEBANK_PASSWORD="your_movebank_user_password"

These variables are inherited by the Slurm job.

2. Write your R script

Example: myRscript.R 

library(move2)

# Get credentials from the env vars and store credentials for this Movebank session
movebank_store_credentials(
  Sys.getenv("MOVEBANK_USER"),
  Sys.getenv("MOVEBANK_PASSWORD")
)
# Check available studies
studies <- suppressWarnings(
  movebank_download_study_info(i_have_download_access = TRUE)
)
# show result
print(studies)

3. Write your bash script

Example: run_myRscript.sbatch 

#!/bin/bash
#SBATCH --job-name=movebank
#SBATCH --time=01:00:00
#SBATCH --mem=4G
#SBATCH --cpus-per-task=1
#SBATCH --output=myRscript_%j.out
#SBATCH --error=myRscript_%j.err

# load R modules
module load R-bundle-CRAN

# launch R script
Rscript myRscript.R

4. Submit the job

srun_-p ceab run_myRscript.sbatch

5. Notes specific to batch execution