ClimateAndMSP

Scripts and data to test whether proactively preparing for climate change-driven shifts in species habitats produces effective ocean plans and whether it imposes tradeoffs.

These scripts are provided in the interests of open science. If you have questions or find errors, please let us know.

Contact:
Malin Pinsky
Rutgers University
malin.pinsky@rutgers.edu

Software versions

Software was executed on a laptop running Mac OS and on a Linux workstation running CentOS.
R version 3.6.1. Main scripting language, with the following packages:
- maps 3.3.0
- mapdata 2.3.0
- maptools 0.9-5
- rgdal 1.4-4
- rgeos 0.5-1
- raster 3.0-2
- sf 0.7-7
- data.table 1.12.8
- beanplot 1.2
- RColorBrewer 1.1-2
- lme4 1.1-21
R version 3.5.3. This version of R was needed to run gurobi, part of the conservation planning algorithm. We used these packages:
- prioritizr 4.1.4
- gurobi 8.1-1
InVEST-3.7.0 and InVEST-3.7.0.post212+hd9612c04a8dc. Used for generating wind and wave energy estimates. The latter development version does not appear to be available anymore, but presumably, the bugs have been fixed in the newer releases.
Gurobi 8.1.1 with an academic license. Used for solving conservation planning problems.

Directory structure

code: scripts that are run using data, data_dl, and output, produce temp, output, figures, and tables
data/natcapt: has data and parameter files generated for this project. Only used for InVEST runs.
- Note that the species range projections from Morley et al. 2018 PLOS ONE are also needed. See below for how they are integrated.
data_dl: has data that is easily downloaded (not tracked by git)
- marineregions/World_EEZ_v10_20180221/: Flanders Marine Institute (2018). Maritime Boundaries Geodatabase: Maritime Boundaries and Exclusive Economic Zones (200NM), version 10. Available online at http://www.marineregions.org/ https://doi.org/10.14284/312
- natcap/WaveEnergy/: Natural Capital project InVEST wave energy data 3.6.0 from here
- natcap/WindEnergy/: Nature Capital project InVEST wind energy data 3.6.0 from here
- natcap/Marine/: Natural Capital project InVEST marine base data 3.6.0 from here
- oceanadapt/: all-regions-full.rds from OceanAdapt version update2019
- sau/: Catch data v47-1 from Sea Around Us for Large Marine Ecosystems 1-3, 5-9, 65
- statcan/: Canadian census population centres, specifically ldpl000b16a_e
- usgs/: US National Map Cities and Towns, specifically citiesx020_nt00007
- WDPA/: World Database on Protected Areas, Aug 2019, from Protected Planet
figures: plotted figures
output: files output by scripts and also used as input for some scripts (tracked by git)
- prioritizr_runs: the conservation plans produced by prioritizr
tables: output tables
temp: temporary files output by scripts (not tracked by git)
temp_figures: temporary figures output by scripts (not tracked by git)

Analysis workflow (roughly... see below for more details)

0.2_averageSBT.r: to set up a climatology
1.0_processWDPA.r: grid the World Database on Protected Areas (WDPA)
1.1_summarizeWDPAbygrid.r: calculate the fraction of protected area in each grid cell
1.2_evalWDPA.r: compare protected areas to projected shifts in species habitats
1.3_WDPAstats.r: summarize the shifts
1.4_compare_WDPA_projections_data.r: Compare the projections to ecological survey observations
3.0_make_NatCap_files.r: make input files for the wind and wave energy calculations by InVEST
3.1_processNatCap.r: process the output from InVEST
5.0_define_CMSP.r: set up the ocean planning analysis
5.0.1_process_species_proj.r: summarize species habitat suitability on the ocean planning analysis grid
5.1_prioritizr.r: run the ocean planning analysis with prioritizr
5.2_evalprioritizr_ensemble.R: compare the ocean plans to the ensemble species projections
5.2_evalprioritizr.r: compare the ocean plans to the individual species projections
5.3_map_species_proj.r: optional maps of species habitat suitability
5.3_plot_and_stats_prioritizr_evaluation.r: some optional plots and analysis examining the ocean plans
6.0_WDPAnetworkstatsbyregion.R: statistics on the protected area networks
6.1_evalRandomNetworks.r: evaluate randomly selected protected areas against shifts in species distribution
6.2_turnover_by_CMSPgrid.R: community change in each ocean planning grid cell
prioritizr_frontier.r: ocean planning runs with a limited total area
plot_figures.r to make figures and some tables

Scripts and files behind figures, tables, and other calculations

All figures and Table S1 are produced by plot_figures.r. The nested lists below indicate which files are needed for each figure or table, as well as which scripts produce those files.

General statistics from plot_figures.r.
1. temp/presmap_*_rcp*_*.csv.gz and temp/biomassmap_*_rcp*_*.csv.gz
  1. 5.0.1_process_species_proj.r
    1. Species distribution projections from Morley et al. 2018 PLOS ONE, available from BCO DMO
2. temp/wdpaturnbyMPAbymod.csv.gz
  1. 1.2_evalWDPA.r
    1. output/wdpa_cov_by_grid0.05.csv.gz
      1. 1.1_summarizeWDPAbygrid.r
        
        temp/wdpa_by_grid0.05_intersect.rds and temp/SPsf2.rds
        
        1.0_processWDPA.r
        
        Species distribution projections from Morley et al. 2018 PLOS ONE: see above
        
        dataDL/WDPA/WDPA_Aug2019_marine-shapefile/WDPA_Aug2019_marine-shapefile
    2. Species distribution projections from Morley et al. 2018 PLOS ONE: see above
Figure 1
1. output/turnover_by_CMSPgrid.csv
  1. 6.2_turnover_by_CMSPgrid.R
    1. temp/presmap_*_rcp*_*.csv.gz: see above
2. output/region_grid.csv.gz
  1. 5.0_define_CMSP.r
    1. temp/SPsf2.rds: see above
    2. dataDL/marineregions/World_EEZ_v10_20180221/eez_v10.shp
    3. dataDL/natcap/Marine/Land/global_polyline.shp
Figure 2
1. output/goalsmetbymod_hist_all.csv and output/goalsmetbymod_2per_all.csv
  1. 5.2_evalprioritizr.r
    1. output/prioritizr_runs/solution_*.csv and output/prioritizr_runs/spp_*.csv
      1. 5.1_prioritizr.r
        
        temp/presmap_*_rcp*_*.csv.gz and temp/biomassmap_*_rcp*_*.csv.gz: see above
        
        Kappa thresholds from Morley et al. 2018 PLOS ONE available here
        
        output/wind_npv.csv.gz and output/wave_npv.csv.gz
        
        3.1_processNatCap.r
        
        ../NatCap_temp/westcoastwind/output/npv_US_millions.tif and ../NatCap_temp/eastcoastwind/output/npv_US_millions.tif
        
        Produced with InVEST 3.7.0 (see below)
        
        dataDL/natcap/WindEnergy/*.*
        
        dataDL/natcap/Marine/*.*
        
        temp/AOI_east.shp and temp/AOI_west.shp, made by 3.0_make_NatCap_files.r, which needs temp/SPsf2.rds (see above)
        
        temp/SPsf2.rds: see above
        
        ../NatCap_temp/westcoastwave/output/npv_usd.tif and ../NatCap_temp/eastcoastwave/output/npv_usd.tif
        
        Produced with InVEST 3.7.0 (see below)
        
        temp/AOI_east.shp and temp/AOI_west.shp: see above
        
        dataDL/natcap/WaveEnergy/*.*
        
        dataDL/natcap/Marine/*.*
        
        output/landgridpts_northamerica.csv, made by 3.0_make_NatCap_files.r, which uses data/natcap/NAmainland_lines.shp, dataDL/usgs/citiesx020_nt00007/citiesx020.shp, and dataDL/statcan/lpc_000b16a_e/lpc_000b16a_e.shp
        
        data/natcap/Machine_Pelamis_Economic_Kimetal2012r0.05.csv
        
        output/fishery_spps.csv
        
        5.0_define_CMSP.r
        
        Species distribution projections from Morley et al. 2018 PLOS ONE: see above
        
        dataDL/sau/*.*
        
        output/region_grid.csv.gz: see above
    2. Kappa thresholds from Morley et al. 2018 PLOS ONE: see above
    3. output/region_grid.csv.gz: see above
    4. temp/presmap_*_rcp*_*.csv.gz and temp/biomassmap_*_rcp*_*.csv.gz: see above
Figure 3
1. output/prioritizr_runs/solution_*.csv: see above
Figure 4
1. temp/frontierall_2019-12-31_075440.csv
  1. prioritizr_frontier.r
    1. temp/presmap_*_rcp*_*.csv.gz and temp/biomassmap_*_rcp*_*.csv.gz: see above
    2. Kappa thresholds from Morley et al. 2018 PLOS ONE: see above
    3. output/wind_npv.csv.gz and output/wave_npv.csv.gz: see above
    4. output/fishery_spps.csv: see above
    5. output/region_grid.csv.gz: see above
2. output/prioritizr_runs/spp_*.csv: see above
Figure 5
1. temp/wdpaturnbyMPAbymod.csv.gz and temp/wdpaturnbynetbymod.csv.gz
  1. 1.2_evalWDPA.r
    1. Species distribution projections from Morley et al. 2018 PLOS ONE: see above
    2. output/wdpa_cov_by_grid0.05.csv.gz: see above
Figure S1
1. temp/frontierall_2019-12-22_071607.csv and temp/frontierall_2019-12-31_075440.csv
  1. prioritizr_frontier.r: see above
  2. output/prioritizr_runs/spp_*.csv: see above
Figure S2
1. output/randMPAs_byBT.csv
  1. 6.1_evalRandomNetworks
    1. output/climatology.csv.gz
      1. 0.2_averageSBT.r
        
        Temperature projections from Morley et al. 2018 PLOS ONE: see above
    2. output/region_grid.csv.gz
    3. Species distribution projections from Morley et al. 2018 PLOS ONE: see above
2. output/MPA_network_stats.csv
  1. 6.0_WDPAnetworkstatsbyregion.R
    1. output/climatology.csv.gz: see above
    2. output/wdpa_cov_by_grid0.05.csv.gz: see above
    3. temp/wdpaturnbyMPAbymod.csv.gz: see above
    4. output/region_grid.csv.gz: see above
Figure S3
1. temp/wdpa_trawlsppobs_byreg.csv.gz and output/MPAvstrawl_NPV_PPV.csv
  1. 1.4_compare_WDPA_projections_data.r
    1. dataDL/oceanadapt/all-regions-full.rds
    2. temp/wdpa_by_spp_projnow.rds
      1. 1.2_evalWDPA.r: see above
    3. output/name_conversions_obs_to_proj.csv
      1. generated by early part of 1.4_compare_WDPA_projections_data.r in an interactive loop
    4. temp/wdpa_by_grid0.05_intersect.rds: see above
    5. dataDL/WDPA/WDPA_Aug2019_marine-shapefile/WDPA_Aug2019_marine-shapefile-polygons.shp: see above
    6. Kappa thresholds from Morley et al. 2018 PLOS ONE: see above
Table S1
1. output/prioritizr_runs/solution_*.csv and output/prioritizr_runs/spp_*.csv: see above
Table S4
1. output/fishery_spps.csv: see above

InVEST runs

These are the detailed program settings used when InVEST was run.

East coast wind
- run with InVEST-3.7.0.post212+hd9612c04a8dc version
- wind data points: dataDL/natcap/WindEnergy/input/Global_EEZ_WEBPAR_90pct_100ms.csv
- area of interest: temp/AOI_east.shp: see above
- Bathymetric DEM: dataDL/natcap/Marine/DEMs/global_dem/w001001.adf
- Land polygon: dataDL/natcap/Marine/Land/global_polygon.shp
- Global wind energy parameters: dataDL/natcap/WindEnergy/input/global_wind_energy_parameters.csv
- turbine type: dataDL/natcap/WindEnergy/input/5_0_turbine.csv
- number of turbines: 16
- min depth: 3m
- max depth: 60 m
- min distance: 0 m
- max distance: 200000 m
- turn on valuation
  - foundation: $2.5M/turbine
  - discount rate 0.05
  - Grid connections: [none]
  - average shore to grid distance: 5 km
  - no price table
  - price of energy: $0.161/kWhr
  - rate of price change: 0.025
West coast wind
- run with InVEST-3.7.0.post212+hd9612c04a8dc version
- wind data points: dataDL/natcap/WindEnergy/input/Global_EEZ_WEBPAR_90pct_100ms.csv
- area of interest: temp/AOI_west.shp: see above
- Bathymetric DEM: dataDL/natcap/Marine/DEMs/global_dem/w001001.adf
- Land polygon: dataDL/natcap/Marine/Land/global_polygon.shp
- Global wind energy parameters: dataDL/natcap/WindEnergy/input/global_wind_energy_parameters.csv
- turbine type: dataDL/natcap/WindEnergy/input/5_0_turbine.csv
- number of turbines: 16
- min depth: 3m
- max depth: 60 m
- min distance: 0 m
- max distance: 200000 m
- turn on valuation
  - foundation: $2.5M/turbine
  - discount rate 0.05
  - Grid connections: [none]
  - average shore to grid distance: 5 km
  - no price table
  - price of energy: $0.161/kWhr
  - rate of price change: 0.025
East coast wave
- run with InVEST-3.7.0.post212+hd9612c04a8dc version
- wave data: dataDL/natcap/WaveEnergy/input/WaveData
- analysis area: Global
- AOI: temp/AOI_east.shp: see above
- Machine performance table: dataDL/natcap/WaveEnergy/input/Machine_Pelamis_Performance.csv
- Machine parameter table: dataDL/natcap/WaveEnergy/input/Machine_Pelamis_Parameter.csv
- Global DEM: dataDL/natcap/Marine/DEMs/global_dem/w001001.adf
- Valuation: yes
  - Grid connections: output/landgridpts_northamerica.csv (see above)
  - Economic table: data/natcap/Machine_Pelamis_Economic_Kimetal2012r0.05.csv
  - # machines: 100
West coast wave
- run with InVEST-3.7.0.post212+hd9612c04a8dc version
- wave data: dataDL/natcap/WaveEnergy/input/WaveData
- analysis area: Global
- AOI: temp/AOI_west.shp: see above
- Machine performance table: dataDL/natcap/WaveEnergy/input/Machine_Pelamis_Performance.csv
- Machine parameter table: dataDL/natcap/WaveEnergy/input/Machine_Pelamis_Parameter.csv
- Global DEM: dataDL/natcap/Marine/DEMs/global_dem/w001001.adf
- Valuation: yes
  - Grid connections: output/landgridpts_northamerica.csv (see above)
  - Economic table: data/natcap/Machine_Pelamis_Economic_Kimetal2012r0.05.csv
  - # machines: 100

Name		Name	Last commit message	Last commit date
Latest commit History 259 Commits
code		code
data/natcap		data/natcap
figures		figures
output		output
tables		tables
.gitignore		.gitignore
ClimateAndMSP.Rproj		ClimateAndMSP.Rproj
LICENSE		LICENSE
README.md		README.md

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