In MVR-GIS/nybem: NY Bight Ecological Model

Introduction

The purpose of this document is to create a package data frame to store the habitat model suitability index values for each model in the NYBEM feasibility study and their labels to streamline model execution and plotting.

Define Suitability Index Values for each Submodel

Freshwater Tidal

# Create the model
NYBEM.fresh.tid <- data.frame(
  salinity.per   = c(0, 20, 100),
  salinity.SIV   = c(1, 0, 0),
  veg.cover.per  = c(0, 57, 100),
  veg.cover.SIV  = c(0.1, 0.5, 1),
  deposition     = c(1, 2, 5),
  deposition.SIV = c(0, 1, 1)
)

# Create model labels
NYBEM.fresh.tid_labels <- data.frame(
  model = "Freshwater, Tidal",
  label = c("Salinity duration (% time > 0.5 psu)", "Vegetation Cover (%)", 
            "Relative Depth"),
  variable = c("salinity", "veg.cover", "deposition")
)

nybem::HSIplotter(NYBEM.fresh.tid, 
           xlab = NYBEM.fresh.tid_labels$label, 
           ylab = NYBEM.fresh.tid_labels$variable)

Estuarine Intertidal

# Create the model
NYBEM.est.int <- data.frame(
  erosion        = c(-50, 10, 50),
  erosion.SIV    = c(1,   1,  0),
  veg.cover.per  = c(0,   100, NA),
  veg.cover.SIV  = c(0.1, 1,   NA),
  deposition     = c(0, 1, NA),
  deposition.SIV = c(1, 0, NA),
  land.use.per   = c(0, 10, 100),
  land.use.SIV   = c(1, 1,  0),
  shoreline.m    = c(0,   100, 500),
  shoreline.SIV  = c(0.5, 1,   1)
)

# Create model labels
NYBEM.est.int_labels <- data.frame(
  model = "Estuarine, Intertidal", 
  labels = c("% Change in Velocity from Existing", "Vegetation Cover (%)",
              "Relative Depth", "Developed Area Within 100m (%)",
              "Distance to Armored Shoreline (m)"),
  variable = c("erosion", "veg.cover", 
                "deposition", "land.use",
                "shoreline")
)

nybem::HSIplotter(NYBEM.est.int, 
           xlab = NYBEM.est.int_labels$labels, 
           ylab = NYBEM.est.int_labels$variable)

Estuarine Subtidal - Hard

# Create the model
NYBEM.est.sub.hard <- data.frame(
  cultch     = c(0, 100, NA, NA, NA, NA, NA, NA),
  cultch.SIV = c(0, 1,   NA, NA, NA, NA, NA, NA),
  MAS        = c(0, 2, 4,    6,   8, 40, NA, NA),
  MAS.SIV    = c(0, 0, 0.05, 0.5, 1, 1,  NA, NA),
  AS         = c(0, 5, 10, 15, 20,  25,  30,  40),
  AS.SIV     = c(0, 0, 1,  1,  0.6, 0.25, 0.1, 0)
)

# Create model labels
NYBEM.est.sub.hard_labels <- data.frame(
  model = "Estuarine, Subtidal, Hard Bottom", 
  label = c("Hard Substrate (%)", "Minimum Annual Salinity (psu)", 
             "Annual Mean Salinity (psu)"),
  variable = c("cultch", "MAS", "AS")
)

nybem::HSIplotter(NYBEM.est.sub.hard, 
           xlab = NYBEM.est.sub.hard_labels$label, 
           ylab = NYBEM.est.sub.hard_labels$variable)

Estuarine Subtidal - Soft, SAV

# Create the model
NYBEM.est.sub.soft.sav <- data.frame(
  substrate.sav      = c(0, 70, 100, NA),
  substrate.sav.SIV  = c(1, 1,  0.1, NA),
  light.PLA          = c(0, 10, 22, 100),
  light.SIV          = c(0, 0,  1,  1),
  vessel.density     = c(0, 1000, 10000, NA),
  vessel.density.SIV = c(1, 1,    0.1,   NA)
)

# Create model labels
NYBEM.est.sub.soft.sav_labels <- data.frame(
  model = "Estuarine, Subtidal, Soft Bottom, Submersed Aquatic Vegetation", 
  label = c("Fine Substrate Composition (%)", "Light Available (%)",
            "Vessel Usage (tracks/year)"),
  variable = c("substrate.sav", "light.PLA", 
               "vessel.density")
)

nybem::HSIplotter(NYBEM.est.sub.soft.sav, 
           xlab = NYBEM.est.sub.soft.sav_labels$label, 
           ylab = NYBEM.est.sub.soft.sav_labels$variable)

Estuarine Subtidal - Soft, Clam

# Create the model
NYBEM.est.sub.soft.clam <- data.frame(
  salinity.clam        = c(0, 12, 12.5, 20, 25, 35, 45),
  salinity.clam.SIV    = c(0, 0, 0.25, 0.75, 1, 1, 0),
  substrate.clam.fines = c(0, 50, 90, 100, NA, NA, NA),
  substrate.clam.SIV   = c(1, 0.75, 0.25, 0,  NA, NA, NA),
  Isav                 = c(0, 0.2, 0.8, 1, NA, NA, NA),
  Isav.SIV             = c(1, 1, 0, 0, NA, NA, NA)
)

# Create model labels
NYBEM.est.sub.soft.clam_labels <- data.frame(
  model = "Estuarine, Subtidal, Soft Bottom, Hard Clam", 
  label = c("Salinity (psu)", "Fine Sediment (%)", 
            "SAV Index"),
  variable = c("salinity.clam", "substrate.clam.fines", 
               "Isav")
)

nybem::HSIplotter(NYBEM.est.sub.soft.clam, 
           xlab = NYBEM.est.sub.soft.clam_labels$label, 
           ylab = NYBEM.est.sub.soft.clam_labels$variable)

Marine Intertidal

# Create the model
NYBEM.mar.int <- data.frame(
  beach.slope.per = c(0, 10, 30, NA),
  beach.slope.SIV = c(1, 1, 0, NA),
  trel            = c(0, 0.25, 0.75, 1.0),
  exp.dur.SIV     = c(0, 1, 1, 0),
  land.use.per    = c(0, 10, 100, NA),
  land.use.SIV    = c(1, 1,  0, NA),
  shoreline.m     = c(0, 100, 500, NA),
  shoreline.SIV   = c(0, 1, 1, NA)
)

# Create model labels
NYBEM.mar.int_labels <- data.frame(
  model = "Marine, Intertidal", 
  label = c("Intertidal Zone Slope (%)", "Relative exposure duration (trel)", 
            "Developed Area Within 100m (%)", 
            "Distance to Armored Shoreline (m)"),
  variable = c("beach.slope", "exp.dur",
               "land.use", "shoreline")
)

nybem::HSIplotter(NYBEM.mar.int, 
           xlab = NYBEM.mar.int_labels$label, 
           ylab = NYBEM.mar.int_labels$variable)

Marine Subtidal

# Create the model
NYBEM.mar.sub <- data.frame(
  velocity           = c(0, 25, 50, 100),
  velocity.SIV       = c(0.6, 1, 1, 0),
  substrate.fines    = c(0, 100, NA, NA),
  substrate.SIV      = c(1, 0.1, NA, NA),
  light.PLW          = c(0, 10, 22, 100),
  light.SIV          = c(0, 0, 1, 1),
  vessel.density     = c(0, 1000, 10000, NA),
  vessel.density.SIV = c(1, 1, 0.1, NA)
)

# Create model labels
NYBEM.mar.sub_labels <- data.frame(
  model = "Marine, Subtidal",
  label = c("Velocity (m)", "Fine Substrate Composition (% fines)", 
            "Percent of Light Available (%)", "Vessel Usage (tracks/year)"),
  variable = c("velocity", "substrate.fines",
               "light", "vessel.density")
)

nybem::HSIplotter(NYBEM.mar.sub, 
           xlab = NYBEM.mar.sub_labels$label, 
           ylab = NYBEM.mar.sub_labels$variable)

Marine Deep

# Create the model
NYBEM.mar.deep <- data.frame(
  salinity.low.dur    = c(0, 50, 100, NA),
  salinity.low.SIV    = c(1, 0, 0, NA),
  velocity.low.change = c(-100, -10, 10, 100),
  velocity.low.SIV    = c(0, 1, 1, 0.8),
  light.PLW           = c(0, 10, 22, 100),
  light.SIV           = c(0, 0, 1, 1),
  vessel.density      = c(0, 1000, 10000, NA),
  vessel.density.SIV  = c(1, 1, 0.1, NA)
)

# Create model labels
NYBEM.mar.deep_labels <- data.frame(
  model = "Marine, Deepwater", 
  label = c("% Time Salinity < 30 psu", "Change in Low Velocity (%)", 
            "Light Penetration (% Reaching Bottom)", "Vessel Usage (tracks/year)"),
  variable = c("salinity.low.dur", "velocity.low.change", 
               "substrate.fines", "vessel.density")
)

nybem::HSIplotter(NYBEM.mar.deep, 
           xlab = NYBEM.mar.deep_labels$label, 
           ylab = NYBEM.mar.deep_labels$variable)

Combine Submodels into List

nybem_submodels <- list(
  NYBEM.fresh.tid         = NYBEM.fresh.tid,
  NYBEM.fresh.tid_labels  = NYBEM.fresh.tid_labels,
  NYBEM.est.int           = NYBEM.est.int,
  NYBEM.est.int_labels    = NYBEM.est.int_labels,
  NYBEM.est.sub.hard      = NYBEM.est.sub.hard,
  NYBEM.est.sub.hard_labels = NYBEM.est.sub.hard_labels, 
  NYBEM.est.sub.soft.sav  = NYBEM.est.sub.soft.sav,
  NYBEM.est.sub.soft.sav_labels = NYBEM.est.sub.soft.sav_labels, 
  NYBEM.est.sub.soft.clam = NYBEM.est.sub.soft.clam,
  NYBEM.est.sub.soft.clam_labels = NYBEM.est.sub.soft.clam_labels,
  NYBEM.mar.int           = NYBEM.mar.int,
  NYBEM.mar.int_labels    = NYBEM.mar.int_labels,
  NYBEM.mar.sub           = NYBEM.mar.sub, 
  NYBEM.mar.sub_labels    = NYBEM.mar.sub_labels,
  NYBEM.mar.deep          = NYBEM.mar.deep,
  NYBEM.mar.deep_labels   = NYBEM.mar.deep_labels
)

Save data to package

usethis::use_data(nybem_submodels,
                  overwrite = TRUE)

MVR-GIS/nybem documentation built on Feb. 9, 2023, 7:03 a.m.