EuroAquaticMacroInverts

This repository contains data and code relating to the study:

The recovery of European freshwater biodiversity has come to a halt

Nature (2023). https://doi.org/10.1038/s41586-023-06400-1

Authors:

Haase, P., D.E. Bowler, N.J. Baker, N. Bonada, S. Domisch, J.R. Garcia Marquez, J. Heino, D. Hering, S.C. Jähnig, A. Schmidt-Kloiber, R. Stubbington, F. Altermatt, M. Álvarez-Cabria, G. Amatulli, D. Angeler, G. Archambaud-Suard, I. Arrate Jorrín, T. Aspin, I. Azpiroz, I. Bañares, J. Barquín Ortiz, C.L. Bodin, L. Bonacina, R. Bottarin, M. Cañedo-Argüelles, Z. Csabai, T. Datry, E. de Eyto, A. Dohet, G. Dörflinger, E. Drohan, K.A. Eikland, J. England, T.E. Eriksen, V. Evtimova, M.J. Feio, M. Ferréol, M. Floury, M. Forcellini, M.A. Forio, R. Fornaroli, N. Friberg, J.-F. Fruget, G. Georgieva, P. Goethals, M.A.S. Graça, W. Graf, A. House, K.-L. Huttunen, T.C. Jensen, R.K. Johnson, J.I. Jones, J. Kiesel,, L. Kuglerová, A. Larrañaga, P. Leitner, L. L'Hoste, M.-H. Lizée, A.W. Lorenz, A. Maire, J.A. Manzanos Arnaiz, B. Mckie, A. Millán, D. Monteith, T. Muotka, J.F. Murphy, D. Ozolins, R. Paavola, P. Paril, F.J. Peñas, F. Pilotto, M. Polasek, J.J. Rasmussen, M. Rubio, D. Sánchez-Fernández, L. Sandin, R.B. Schäfer, A. Scotti, L.Q. Shen, A. Skuja, S. Stoll, M. Straka, H. Timm, V.G. Tyufekchieva, I. Tziortzis, Y. Uzunov, G.H. van der Lee, R. Vannevel, E. Varadinova, G. Várbíró, G. Velle, P.F.M. Verdonschot, R.C.M. Verdonschot, Y. Vidinova, P. Wiberg-Larsen, E.A.R. Welti

Metadata file:

AquaticMacroInvert_metadata.xls :

• Contains information on data providers, site characteristics, and the number of sites from each country
• Two tabs within this metadata spreedsheet contain metadata for the two csv files (in the outputs folder):
  • All_indices_benthicMacroInverts_AllYears_alienzeros.csv (metadata tab: metadata_siteyear)
  • All_siteLevel.csv (metadata tab: metadata_sites)

raw-data folder:

• RawData_metadata.docx : Provides metadata regarding raw data files

• csvs_each_dataset folder: Contains raw taxonomic composition data for all included studies

outputs folder:

• All_indices_benthicMacroInverts_AllYears_alienzeros.csv : Contains data for each site and year on:

  • taxonomic diversity metrics

• All_siteLevel.csv : Contains data for each site on slopes of functional and taxonomic diversity indices and environmental drivers

• outputs_metaAnaylsis folder: Trend meta-analysis model outputs

• outputs_movingWindow folder: Moving window analysis outputs

• outputs_driver folder: Driver analysis outputs

• outputs_sensitivity folder: Sensitivity analyses outputs including:

  • high threshold moving window analysis (HTMW2)
  • one-country removal effects (Jackknife)
  • meta-analysis model comparisions (metaanalysisModelComparison)
  • site level high threshold moving window analysis (siteLevel_HTMW)
  • driver and moving window analyses only for sites with taxonomic resolution to species level (SppLevel_outputs)
  • taxonomic resolution and seasonality sensitivity analyses outputs (TaxonomicSeason)

• TaskIDs folder: Task IDs for running models and model estimates

• ClimateModel_stan folder: Contains outputs of models calculating temperature and precipitation trends

R folder

• Initial_Biodiversity_FuncTrait_and_climate_calcs folder: Contains scripts to calculate taxonomic and functional trait metrics for each site year and calculate temperature and precipitation trends

• stan_models folder: Contains scripts of all stan models used in analyses

• trend_metaAnalysis folder: Contains the following scripts:

  • HPC_macroinverts_stanmodels : Models to calculate trends for each biodiversity metric and each of the 1816 sites
  • HPC_Meta_analysis : Meta-analysis models to synthesize the site-level data using the output of the previous step and get overall trend for each metric (Trend ~ 1 + (1|study_ID) + (1|Country)
  • HPC_modelchecking : Examining meta-analysis model fit parameters and calculating probability increasing/decreasing for each biodiversity metric

• MovingWindow folder: Contains the following scripts:

  • HPC_MovingWindow_sites : Models to calculate trends for each site within each window and biodiversity metric in moving window analysis
  • HPC_Meta_analysis_movingwindow : Models to calculate overall estimates of trends within each window and biodiverisity metric
  • MetaMeta_movingwindowEsts_Yr : Models to calculate overall linear year effects on biodiversity trajectories in moving window analyses

• Driver folder: Contains the following scripts:

  • HPC_Meta_analysis_drivers : Models to caluculate driver effects on biodiversity metrics using site-level data
  • Modelchecking_Drivers_horseshoePriors : Examining driver model fit parameters

• Sensitivity folder: Contains scripts for sensitivity checking models including:

  • effects of trends within countries (Country_effects)
  • high threshold moving window analysis (HTMW)
  • using a one stage model rather than the two stage meta-analysis model for trend estimates (OneStage_models)
  • effects of taxonomic resolution for the moving window analysis and claculating the proportion of pos/neg trends/ window (checking_MovingWindow_parameters)
  • effects of taxonomic resolution and seasonality on trend estimates (HPC_Sensitivity_analysis)
  • examing driver model outputs for sites with taxa IDed to species level only (Modelchecking_Drivers_sppLevel_horseshoe)

• HPC_combine_site_trends script: Concatenates outputs for many analyses including:

  • biodiverity trends
  • meta-analysis
  • moving window analysis
  • driver analysis
  • sensitivity analyses

plots folder

• Online Figures.docx : Includes all additional online figures not included in main text or Extended Data

• Supplementary Table 2 : Contains information on time series locations, durations, and site characteristics

• Fig1 folder: Contains scripts, data, and icons used to make Figure 1

• Fig2_DensityPlots folder : Contains scripts and plots related to meta-analysis trend results

• Fig3_movingWindow folder: Contains scripts and plots related to the moving window analyses

• Fig4_drivers folder: Contains scripts and plots related to driver analyses

• descriptive_plots folder: Contains scripts and plots descriping data distributions and correlations

• Sensitivity folder: Contains scripts and plots for sensitivity analyses regarding:

  • one-country removal effects (Jackknife)
  • meta-analysis model comparisions (one stage, two stage weighted and unweighed)
  • effects of sampling years & start year
  • effects of seasonality
  • effects of taxonomic resolution