This repository is for the synthesis paper 'Widespread ecological responses and cascading effects of the record-breaking 2021 western North American heatwave'
Aphids
Script: "scripts/processing/figure 3/fig3_aphids-on-berries.R"
Input: "data/tidy_data/fig3/aphids-on-berries.csv"
Output: "data/tidy_data/fig3/meta_analysis/aphids_meta.Rdata"
Balanus
Script: "scripts/processing/figure 3/fig3_balanus_shade_vs_sun.R"
Input: "data/tidy_data/fig3/balanus_mortality_pruth.csv"
Output:
- "data/tidy_data/fig3/meta_analysis/balanus_meta.Rdata"
- "figures_tables/raw figures/fig3_balanus_pruthbay_by_exposure.jpg"
Bats
Script: "scripts/processing/figure 3/fig3_condensed_bat-data.R"
Input: "data/tidy_data/fig3/bat.2020.2021.short.csv"
Output: "data/tidy_data/fig3/meta_analysis/bat_meta.Rdata"
Hawks
Script: "scripts/processing/figure 3/fig3_hawks.R"
Input: "data/tidy_data/fig3/FEHAall2020_2022_distancetravelledovertime_filledin_June25toJuly7.csv"
Output:
- "figures/maggie_proto/hawk_fig.png"
- "data/tidy_data/fig3/meta_analysis/hawks_meta.Rdata"
Honeybee
Script: "scripts/processing/figure 3/fig3_honeybees.R"
Input: "data/tidy_data/fig3/hive-weight-summary-by-period.csv"
Output: "data/tidy_data/fig3/meta_analysis/honeybee_meta.RData"
Interior shrubs
Script: "scripts/processing/figure 3/fig3_interior_shrubs.R"
Input: "shrubdata.csv"
Output: "data/tidy_data/fig3/meta_analysis/interiorshrubMAS_meta.RData"
Lupines
Script: "scripts/processing/figure 3/fig3_lupines_fruits.R"
Input: "data/tidy_data/fig3/LUPLATheatdome_fruits_20_21.csv"
Output: "data/tidy_data/fig3/meta_analysis/lupine_meta.Rdata"
Mammals
Script: "scripts/processing/figure 3/fig3_mammals.R"
Input: "data/tidy_data/fig3/ct_hd_temp_v_detections_fig_data.csv"
Output: "data/tidy_data/fig3/meta_analysis/mammals_meta.Rdata"
Mytilus
Script: "scripts/processing/figure 3/fig3_mytilus_mortality_under_fucus.R"
Input: "data/tidy_data/fig3/mytilus_mortality.csv"
Output:
-"figures_tables/raw figures/fig3_mytilus_mortality_fucus_presence.jpg"
- "data/tidy_data/fig3/meta_analysis/mytilus_meta.Rdata"
Nucella
Script: "scripts/processing/figure 3/fig3_nucella_mortality.R"
Input: "data/tidy_data/fig3/nucella_mortality.csv"
Output:
- "figures_tables/raw figures/nucella_mort_pre_vs_post.jpg"
- "data/tidy_data/fig3/meta_analysis/nucella_meta.Rdata"
Phyllospadix
Script: "scripts/processing/figure 3/fig3_phyllospadix_calvert.R"
Input: "data/tidy_data/fig3/Hakai_surfgrass_density_flowering.csv"
Output:
- "data/tidy_data/fig3/meta_analysis/phyllospadix_meta.Rdata"
Scoter
Script: "scripts/processing/figure 3/fig3_surf_scoter.R"
Input: "data/tidy_data/fig3/full_scoter.csv"
Output:
- "figures_tables/raw figures/surfscoter_deltasd_binary.png"
- "figures_tables/raw figures/surfscoter_deltacts.png"
- "data/tidy_data/fig3/meta_analysis/scoter_meta.RData"
Semibalanus
Script: "scripts/processing/figure 3/fig3_semibalanus.R"
Input:
- "./raw_data/semibalanus/SBHW_SHADE_surveys.csv" *** .. Hesketh and Harley
- "./raw_data/semibalanus/SBHW_SHADE_PlotInfo.csv" Output:
- "./tidy_data/meta_analysis/semibalanus_meta.Rdata"
Songbirds
Script: "scripts/processing/figure 3/fig3_semibalanus.R"
Input:
- "data/tidy_data/fig3/passerine_BirdNET_2021.csv"
Output: - "data/tidy_data/fig3/meta_analysis/songbirds_meta.Rdata"
Algae
Script: "scripts/processing/figure 3/fig3_baumlab-algae.R"
Input: "./raw_data/heatdome_seaweeds_baumlab.csv" Sandra Emry
Output: "data/tidy_data/fig3/meta_analysis/algae_meta.Rdata"
Script:
- "scripts/processing/figure 3/meta_analysis_prep.R"
Input data:
- "data/tidy_data/fig3/meta_analysis/aphids_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/balanus_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/bat_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/hawks_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/honeybee_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/interiorshrub_meta.Rdata" # not used in script
- "data/tidy_data/fig3/meta_analysis/lupine_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/mammals_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/mytilus_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/nucella_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/phyllospadix_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/scoter_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/semibalanus_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/songbirds_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/algae_meta.Rdata"
- "data/tidy_data/fig3/meta_analysis/interiorshrubMAS_meta.RData" # not used in script
Output data:
- "data/tidy_data/fig3/meta_analysis/heatdome_meta.csv"
Scripts, to be run in numbered order, in scripts/streamflow_scripts:
- 01_Hydro_station_metadata
- 02_streamflow
- 03_Collating_2021_streamflow_data
- 04_waterflow_metrics
- 05_extract temperature_points
- 06_all_data_compiled
- 07_streamflow_visualization
then run: scripts/main_figures/fig6_wildfire_area_and_streamflow
Input data:
- data/streamflow_wildfires/input/Hydro_station_metadata.csv
- data/streamflow_wildfires/input/week_before_htdome_daymet_tmax.tif
- data/streamflow_wildfires/input/tmax_deviation_new5days.tif
- data/streamflow_wildfires/input/tmax_deviation_max_new5days.tif
- data/streamflow_wildfires/input/lst_deviation_new5days.tif
- data/streamflow_wildfires/input/lst_deviation_max_new5days.tif
- data/streamflow_wildfires/input/glacier_snowcover_per_watersheds.csv
- data/streamflow_wildfires/input/snowcover_per_watersheds.csv
- data/streamflow_wildfires/processed_data/wildfire_stats_2000_2020.csv
- data/streamflow_wildfires/processed_data/wildfire_stats_2016_2020.csv
- data/streamflow_wildfires/processed_data/wildfire_stats_2021.csv
- data/streamflow_wildfires/watersheds/WSC_Basinsgdb/ [all files]
- data/streamflow_wildfires/waterflow_2021/ [all files]
The linear models are created in script 06_all_data_compiled. In order to easily run this script in isolation from other scripts we provide:
Intermediate data object:
- data/streamflow_wildfires/processed_data/xvar_streamflow.csv
Treehole insects
Script: "scripts/Table2/Treehole_mortality.R"
Input:
- data/raw_data/Table2/inverts_clean_2021.csv
- data/raw_data/Table2/treehole_2022.csv
Output: - "data/Table2/treehole_invertebrate_mortality.csv"
Figure 1
Manually compiled within ArcGIS
Figure 2
Script: scripts/main_figures/fig_TPC_conceptual.R
Input data: 10-day mean air temperature leading up to heat dome period:
"data/fig2_raster_data/pre_heatdome_norm_avg_Tavg.tif" # Historical "data/fig2_raster_data/pre_2021heatdome_avg_Tavg.tif" # 2021
Avg surface temperature during period of heat dome; assumed = leaf temperature:
"data/fig2_raster_data/heatdome_norm_avg_LST_proj.tif" # Historical "data/fig2_raster_data/heatdome_2021_avg_LST_proj.tif"# 2021
Avg VPD during period of heat dome:
"data/fig2_raster_data/heatdome_norm_avg_VPD.tif"# Historical "data/fig2_raster_data/heatdome_2021_avg_VPD.tif"# 2021
Output figure: fig2.png
Figure 3 and Extended Data Table 2
Script: "scripts/main_figures/fig3meta_analysis.R""
Input:
- "data/tidy_data/fig3/meta_analysis/heatdome_meta.csv"
(the construction of this dataset is detailed in Steps 1&2 under "Meta-analysis")
Output:
- "figures_tables/fig3.png"
- "figures_tables/supplement/extendeddatatable2.csv"
Figure 4 is a photo montage, so no underlying data
Figure 5
Script: scripts/main_figures/fig5_GPP_map.R
Input data: 10-day mean air temperature leading up to heat dome period:
- "data/fig2_raster_data/pre_heatdome_norm_avg_Tavg.tif" # Historical
- "data/fig2_raster_data/pre_2021heatdome_avg_Tavg.tif" # 2021
Avg surface temperature during period of heat dome; assumed = leaf temperature:
- "data/fig2_raster_data/heatdome_norm_avg_LST_proj.tif" # Historical
- "data/fig2_raster_data/heatdome_2021_avg_LST_proj.tif"# 2021
Avg VPD during period of heat dome:
- "data/fig2_raster_data/heatdome_norm_avg_VPD.tif"# Historical
- "data/fig2_raster_data/heatdome_2021_avg_VPD.tif"# 2021
Output figure: fig5.png
Figure 6 See "Analysis if streamflow" section for input data and script pipeline.
Output:
- "figures_tables/raw figures/regression.tiff"
- "figures_tables/raw figures/juneregression.tiff"
- "figures_tables/raw figures/augregression.tiff"
- "figures_tables/Figure6.tiff"
Extended Data Figure 1-3,6
Manually compiled within ArcGIS
Extended Data Figure 4
Script: "scripts/processing/figure 3/fig3_honeybees.R"
Input: "data/tidy_data/fig3/all.hives.2.filtered.csv"
Output: "figures_tables/supplement/hive-ambient-temp.png"
Extended Data Figure 5 this is a photomontage so no data compilation