CAGED: A cross-ecosystem synthesis exploring the consequences of consumer loss on community variability

Principal Investigators:

• Jamie McDevitt-Irwin
• Kelly Speare
• Sally Koerner

• 000_group-member-shortcut -- Download raw data, the data key, site-level metadata, or tidy outputs of core workflow scripts from the group's Shared Drive
  • Requires access to Drive & authentication with the googledrive R package
• 00_setup -- Do all setup tasks used by 2 or more other scripts (e.g., create folders)
• 01_harmonize -- Standardize all raw data format using data key and combine into single output
  • See ?ltertools::standardize for details
• 02_quality-control -- Do general QC of data
  • E.g., standardize treatments/dates, ensure unique design level designations, identify study years
• 03_filter -- Remove rows that are not useful for the current project scope
  • E.g., all but last year of sampling, no confounding treatments
• 04_zero-fill -- Zero fill community data
  • Assumes any taxon identified in only one replicate of an experiment is truly absent from other reps of the same experiment
• 05-A_calc-beta -- Calculate beta dispersion at various spatial/temporal scales
• 05-B_calc-gamma -- Calculate gamma diversity within experiment across and within treatment
• 05-C_calc-alpha -- Calculate alpha diversity (richness) at all design levels
• 05-D_calc-dominance -- Calculate dominance (Berger Parker) at all design levels
• 06-A_compare-treat-mean-beta -- Calculate mean difference and log response ratios (LRR) between caging treatment beta dispersions
• 06-B_compare-treat-gamma -- Calculate difference & LRR for between caging treatment gamma richness
• 06-C_compare-treat-alpha -- Calculate difference & LRR for between caging treatment alpha diversity (i.e., richness)
• 06-D_compare-treat-dominance -- Calculate difference & LRR for between caging treatment dominance
• 07_tidy-metadata -- Do QC on metadata file and check for mismatches with beta dispersion data
• 08-A_join-data -- Join site-level metadata, beta dispersion (un-averaged), gamma richnes, alpha richness, and dominance
• 08-B_join-effect-sizes -- Join site-level metadata, treament/experiment means of beta dispersion, alpha diversity, gamma richness, and dominance
• 09_prepare-for-stats -- Calculate effect size and streamline data to only bits needed for current analysis
• 10a_raw-data-figs --
• 10b_sample-size --
• 10c_stats --
• 99_upload -- Upload outputs of core workflow to Drive (file size-permitting)

• LTER Scientific Computing Team website
• NCEAS' Resources for Working Groups
• CAGED Working Group Shared Drive