Code and data for "Long-term declines and recovery of meadow area across the world’s seagrass bioregions"

Citation: Dunic, J. C., Brown, C. J., Connolly, R. M., Turschwell, M. P., & Côté, I. M. (2021). Long-term declines and recovery of meadow area across the world’s seagrass bioregions. Global Change Biology, n/a(n/a). https://doi.org/10.1111/gcb.15684

This repository includes the code and data used in the above paper and should reproduce all figures, tables, and supplemental figures/tables found in the paper.

Contributors to this code base, including the use of GAMs for the reconstruction of seagrass meadow area time series: cbrown5 and mpturschwell.

Scripts

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Reproduce overall results:

00_get-results.R

• Sources scripts in the order required to reproduce results.

Load functions:

01_functions.R

• contains most of the key functions used in the analysis and construction of figures, some functions are still found with in scripts (originally there to aid with troubleshooting)

Reconstruct time series and prepare data for visualisation

02_analysis-data-prep.R

• Applies some unit conversions, provides factor levels, applies Short et la. 2007 bioregions.

02_gam-interpolation.R

• Reconstruct time series for each meadow using a GAM fit to each bioregion. A GAM was fit for the Mediterranean, but excluded 16 sites with only two sampled time points (insufficient data to fit the GAM). These sites were reconstructed using linear impuation.

03_decadal_data_prep.R

• Prepare the data for the rest of the analyses. Formats factors/names/colours and combines site covariates with the decadal estimates from the reconstructions in <02_gam-interpolation.R>

Produce figures and tables

04_bioregional_GAM_trends.R

• Plots the bioregional GAM fits (Figure 2).

04_descriptive_stats.R

• Produce some summary values referenced in text and some supplementary figures.

04_driver-attributions.R

• Get summary information and plot driver/attribution figures (Figure 4 & 5) in main text and supplementary information.

04_net-change.R

• Calculate net change (Table 2) values and produce supplementary figures to show net change across decades.

04_site-map.R

• Produce map (Figure 1) showing sites in this study, sites from Waycott et al .2009, global seagrass distribution, and Short et al. 2007 bioregions. Short bioregions were converted to a shapefile by the GLOW team.

04_status_plots.R

• Produce status plots to visualise the individual meadow variablity across bioregions (Figure 3) and supplementary status plots.

Produce results files

05_Figures.Rmd 05_Tables.Rmd

• Render the main text figure and tables to word documents. The figures are all created in the 04_XX.R scripts. Table 1 is contained in this script.

Supplementary results

06_Supplementary_figures.Rmd 06_Supplementary_tables.Rmd

• Render the supplementary figures and tables to word documents. The figures are all created in the 04_XX.R scripts.