Atlas-Tools

Relative paths are used for most files, where the SEACAR_Trend_Analyses repository is assumed to be in the same parent folder as Atlas-Tools. This can be achieved by cloning both repositories into a “SEACAR GitHub” folder on the desktop. The following dependencies are downstream of the individual habitat analyses performed within SEACAR_Trend_Analyses, which should all be performed prior to Atlas-Tools implementation.

ModelAggregation

Consists of the following files and their dependencies:

• run.R (executes the analyses)

  • WebsiteParameters (via SEACAR package)

• sav_ma_models.R

  • SAV_BBpct_LMEresults_All.xlsx

  • SAV models (SEACAR_Trend_Analyses/SAV/output/models)

    • SAV_BBpct_... .rds

    • Failedmodslist.rds

  • Simplified SAV .rds trendplots (SEACAR_Trend_Analyses/SAV/output/Figures/BB)

• disc_model_agg_bayesian_parallel.R

  • WQ_Discrete_All_KendallTau_Stats.txt

  • Only for diagnostic plots:

  • Skt_stats_disc (only for diagnostics - SEACAR_Trend_Analyses/WQ_Cont_Discrete/output/tables/disc/skt_stats_disc.rds)

  • Rds objects in SEACAR_Trend_Analyses/WQ_Cont_Discrete/output/figuredata/

• TrendStatusGeneration.Rmd

  • WQ_agg_results.xlsx (created in disc_model_agg_bayesian_parallel.R above)

  • WQ_Discrete_All_KendallTau_Stats.txt

  • all_SAV_MA_Results.xlsx (created in sav_ma_models.R above)

  • Nekton_SpeciesRichness_MA_Overall_Stats.txt

  • Nekton_SpeciesRichness_MA_Yr_Stats.txt

  • CoastalWetlands_SpeciesRichness_MA_Overall_Stats.txt

  • CoastalWetlands_SpeciesRichness_MA_Yr_Stats.txt

  • Coral_SpeciesRichness_MA_Overall_Stats.txt

  • Coral_SpeciesRichness_MA_Yr_Stats.txt

  • Coral_PC_LME_Stats.txt

  • Oyster_All_GLMM_Stats.txt

  • output/disc_model_results.csv (created in disc_model_agg_bayesian_parallel.R above)

  • ChangeAnalysis_ChangeResultTable_YYYY.xlsx (provided by USF)

tableDescriptions

Consists of the following files and their dependencies:

• run.R (executes the analyses)

  • WebsiteParameters (via SEACAR package)

  • ManagedAreas (via SEACAR package)

• Each habitat has a .csv file which contains the table descriptions which are generated in-line within each habitat analysis. These files are then combined into the final AtlasDescriptions.xlsx output file.