TempSynthesis

Analysis of water temperature data from the Sacramento San-Joaquin Delta

Data have been downloaded from CDEC (https://cdec.water.ca.gov/) and cleaned.

Integrated datasets are published at: https://portal.edirepository.org/nis/mapbrowse?packageid=edi.591.2

Species thresholds are published at: https://portal.edirepository.org/nis/mapbrowse?scope=edi&identifier=1286&revision=3

Code asssociated with Water Temperature Thresholds Manuscript

• Go to manuscript_code folder for most up-to-date code.

Data

• Data/StationsMetadata.csv: Metadata about stations - lat/lon, start and end date of stations, names
• Data/Temp_filtered.rds: Original QA/QCed filtered water temperature dataset
• Data/temp10years_20230613.rds: Hourly dataset filtered down to desired stations and time periods
• Data/tempMonthly.rds: Monthly temperature dataset used for trend modeling
• Data/SpeciesThresholds.xlsx: Species temperature thresholds
• Data/daysExceedanceUpperDataForPlotting.csv: Calculations for each species days exceeding upper thresholds
• Data/daysExceedanceDataForPlotting.csv: Calculations for each species days exceeding lower thresholds
• Data/emmeans_results/: Emmeans tables
• RosiesRegionsEdited: Shapefile of regions used for map and analysis

Code

• prepare_datasets.Rmd: Script to filter dataset based on the location of the station and the amount of missing data for the station; creates annual, daily, monthly datasets including appropriate summary stats
• join_stations_to_regions.Rmd: Script to join Rosie's regions shapefile to stations
• make_manuscript_map.Rmd: Script to make original map - this got replaced by the cluster analysis map, which is based on this map.
• tempclusters.Rmd: Cluster analysis
• model_temperature_trends.Rmd: Mixed Model of maximum and minimum water temperature trends
• model_native_nonnative.Rmd: Mixed Model of native/non-native and listed/unlisted species differences
• plot_days_exceedance_boxplot.Rmd: Script to create days exceedance boxplots
• plot_fish_absence_presence_vulnerability.Rmd: Script to create vulnerability tile plot
• model_temperature_trends.Rmd: Mixed Model of maximum and minimum water temperature trends
• stationheatmaps.R: Script to create heat map looking at station and regional suitability by day of year (identify no recovery areas)

Figures

• model_validation_plots: contain model validation plots for listed status model, maximum temperature model, minimum temperature model
• additional_figures: contain heat map plots for data that could be of interest but were not in the manuscript
• Other figures in the Figures folder are part of the manuscript.