habitat_scale_analysis Author: Herbert Leavitt Last Updated: 6/3/2025
Overview: This repository contains exemplar datasets and code for analyzing the relationship between habitat structure and species abundance across multiple spatial scales in a rapidly changing estuarine environment near Port Fourchon, Louisiana. Due to file size limitations on GitHub, this repository is designed to show examples of data inputs and produces, but does not contain the complete workflow. The complete dataset is available on BCODMO at: DOI:10.26008/1912/bco-dmo.948167.1
Repository Structure:
- landscape_analysis/: Scripts and data related to landscape-level habitat analysis. Note that these analyses must be run on a high performance computing cluster. Bash code is SLURM submission script to the cluster that identifies code to be run and assigns resources to the job.
- species_analysis/: Scripts and data focused on species abundance and distribution analysis.
- .gitignore: Specifies files and directories to be ignored by Git.
Usage:
-
Clone the repository: git clone https://github.com/heleavitt/habitat_scale_analysis.git
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Navigate to the cloned directory: cd habitat_scale_analysis
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Explore the landscape_analysis and species_analysis directories for relevant scripts and data.
Requirements:
Python Packages:
- geopandas
- pandas
- numpy
- shapely
- pathlib
- gc
- concurrent.futures
- glob
- os
R Environment: This analysis was performed using R version 4.3.2
R Packages (attached or used directly):
- mgcv_1.9-0
- nlme_3.1-163
- gam_1.22-4
- foreach_1.5.2
- spdep_1.3-5
- sf_1.0-16
- spData_2.3.1
- lubridate_1.9.3
- forcats_1.0.0
- stringr_1.5.1
- dplyr_1.1.4
- purrr_1.0.2
- readr_2.1.4
- tidyr_1.3.0
- tibble_3.2.1
- ggplot2_3.5.1
- tidyverse_2.0.0
- scales_1.3.0
- statmod_1.5.0
- pscl_1.5.9
R Packages (loaded via namespace only):
- gtable_0.3.4
- lattice_0.21-9
- tzdb_0.4.0
- vctrs_0.6.5
- tools_4.3.2
- generics_0.1.3
- proxy_0.4-27
- fansi_1.0.5
- pkgconfig_2.0.3
- Matrix_1.6-1.1
- KernSmooth_2.23-22
- lifecycle_1.0.4
- compiler_4.3.2
- farver_2.1.1
- deldir_2.0-4
- munsell_0.5.0
- codetools_0.2-19
- class_7.3-22
- pillar_1.9.0
- crayon_1.5.2
- MASS_7.3-60
- classInt_0.4-10
- wk_0.9.1
- iterators_1.0.14
- boot_1.3-28.1
- tidyselect_1.2.1
- stringi_1.8.2
- labeling_0.4.3
- grid_4.3.2
- colorspace_2.1-0
- cli_3.6.1
- magrittr_2.0.3
- utf8_1.2.4
- e1071_1.7-14
- withr_3.0.2
- sp_2.1-3
- timechange_0.2.0
- hms_1.1.3
- viridisLite_0.4.2
- s2_1.1.6
- rlang_1.1.2
- Rcpp_1.0.11
- glue_1.6.2
- DBI_1.1.3
- rstudioapi_0.15.0
- R6_2.5.1
- units_0.8-5
Contact: For questions or collaboration inquiries, please contact Herbert Leavitt.