R: Stochastic collision risk model for a single species and one...

stoch_crm {stochLAB}

R Documentation

Stochastic collision risk model for a single species and one wind farm scenario

Description

Runs a Stochastic Collision Risk Model (SCRM) for estimating the number of in-flight collisions with offshore windfarm turbines, for given species and windfarm scenario. Core calculations follow the work developed by Masden (2015). See Background and Updates section below for more details.

Usage

stoch_crm(
  model_options = c("1", "2", "3", "4"),
  n_iter = 1000,
  flt_speed_pars,
  body_lt_pars,
  wing_span_pars,
  avoid_bsc_pars = NULL,
  avoid_ext_pars = NULL,
  noct_act_pars,
  prop_crh_pars = NULL,
  bird_dens_opt = c("tnorm", "resample", "qtiles"),
  bird_dens_dt,
  flight_type,
  prop_upwind,
  gen_fhd_boots = NULL,
  site_fhd_boots = NULL,
  n_blades,
  air_gap_pars,
  rtr_radius_pars,
  bld_width_pars,
  bld_chord_prf = chord_prof_5MW,
  rtn_pitch_opt = c("probDist", "windSpeedReltn"),
  bld_pitch_pars = NULL,
  rtn_speed_pars = NULL,
  windspd_pars = NULL,
  rtn_pitch_windspd_dt = NULL,
  trb_wind_avbl,
  trb_downtime_pars,
  wf_n_trbs,
  wf_width,
  wf_latitude,
  tidal_offset,
  lrg_arr_corr = TRUE,
  xinc = 0.05,
  yinc = 0.05,
  out_format = c("draws", "summaries"),
  out_sampled_pars = FALSE,
  out_period = c("months", "seasons", "annum"),
  season_specs = NULL,
  verbose = TRUE,
  log_file = NULL,
  seed = NULL
)

Arguments

`model_options`	Character vector, the model options for calculating collision risk (see Details section below).
`n_iter`	An integer. The number of iterations for the model simulation.
`flt_speed_pars`	A single row data frame with columns `mean` and `sd`, the mean and standard deviation of the species flying speed, in metres/sec. Assumed to follow a Truncated Normal with lower bound at 0 (tnorm-lw0).
`body_lt_pars`	A single row data frame with columns `mean` and `sd`, the mean and standard deviation of the species body length, in metres. Assumed to follow a tnorm-lw0 distribution.
`wing_span_pars`	A single row data frame with columns `mean` and `sd`, the mean and standard deviation of the species wingspan, in metres. Assumed to follow a tnorm-lw0 distribution.
`avoid_bsc_pars`, `avoid_ext_pars`	Single row data frames with columns `mean` and `sd`, the mean and standard deviation of the species avoidance rate to be used in the basic model (Options 1 and 2) and extended model (Options 3 and 4) calculations (see Details section). Avoidance rate expresses the probability that a bird flying on a collision course with a turbine will take evading action to avoid collision, and it is assumed to follow a Beta distribution.
`noct_act_pars`	A single row data frame with columns `mean` and `sd`, The mean and standard deviation of the species nocturnal flight activity level, expressed as a proportion of daytime activity levels, and assumed to be Beta distributed.
`prop_crh_pars`	Required only for model Option 1, a single row data frame with columns `mean` and `sd`. The mean and standard deviation of the proportion of flights at collision risk height derived from site survey, assumed to be Beta distributed.
`bird_dens_opt`	Option for specifying the random sampling mechanism for bird densities: `"tnorm"`: Sampling of density estimates from a tnorm-lw0 distribution (default value), `"resample"`: Re-sample draws of bird density estimates (e.g. bootstrap samples), `"qtiles"`: Sampling from a set of quantile estimates of bird densities.
`bird_dens_dt`	A data frame with monthly estimates of bird density within the windfarm footprint, expressed as the number of daytime in-flight birds/km^2 per month. Data frame format requirements: If `bird_dens_opt = "tnorm"`, `bird_dens_dt` must contain the following columns: `month`, (unique) month names, `mean`, the mean number of birds in flight at any height per square kilometre in each month, `sd`, idem, for standard deviation. If `bird_dens_opt = "resample"`, `bird_dens_dt` columns must be named as months (i.e. `Jan`, `Feb`, ...), each containing random samples of monthly density estimates. If `bird_dens_opt = "qtiles"`, `bird_dens_dt` must comply with: First column named as `p`, giving reference probabilities, Remaining columns named as months (i.e. `Jan`, `Feb`, ...), each giving the quantile estimates of bird density in a given month, for the reference probabilities in column `p`.
`flight_type`	A character string, either 'flapping' or 'gliding', indicating the species' characteristic flight type.
`prop_upwind`	Numeric value between 0-1 giving the proportion of flights upwind - defaults to 0.5.
`gen_fhd_boots`	Required only for model Options 2 and 3, a data frame with bootstrap samples of flight height distributions (FHD) of the species derived from general (country/regional level) data. FHD provides relative frequency distribution of bird flights at 1-+ -metre height bands, starting from sea surface. The first column must be named as `height`, expressing the lower bound of the height band (thus it's first element must be 0). Each remaining column should provide a bootstrap sample of the proportion of bird flights at each height band, with no column naming requirements. NOTE: generic_fhd_bootstraps is a list object with generic FHD bootstrap estimates for 25 seabird species from Johnson et al (2014) doi:10.1111/1365-2664.12191 (see usage in Example Section below).
`site_fhd_boots`	Required only for model Option 4, a data frame similar to `gen_fhd_boots`, but for FHD estimates derived from site-specific data.
`n_blades`	An integer, the number of blades in rotor (`b`).
`air_gap_pars`	A single row data frame with columns `mean` and `sd`, the mean and standard deviation of the tip clearance gap, in metres, i.e. the distance between the minimum rotor tip height and the highest astronomical tide (HAT). Assumed to follow a tnorm-lw0 distribution.
`rtr_radius_pars`	A single row data frame with columns `mean` and `sd`, the mean and standard deviation of the radius of the rotor, in metres. Assumed to follow a tnorm-lw0 distribution.
`bld_width_pars`	A single row data frame with columns `mean` and `sd`, the mean and standard deviation of the maximum blade width, in metres. Assumed to be tnorm-lw0 distribution.
`bld_chord_prf`	A data frame with the chord taper profile of the rotor blade. It must contain the columns: `pp_radius`, equidistant intervals of radius at bird passage point, as a proportion of `rotor_radius`, within the range `[0, 1]`. `chord`, the chord width at `pp_radius`, as a proportion of `blade_width`. Defaults to a generic profile for a typical modern 5MW turbine. See `chord_prof_5MW()` for details.
`rtn_pitch_opt`	a character string, the option for specifying the sampling mechanism for rotation speed and blade pitch: `"probDist"`: sample rotation speed and blade pitch values from a tnorm-lw0 distribution (default value). `"windSpeedReltn"`: generate rotation speed and blade pitch values as a function of wind speed intensity.
`bld_pitch_pars`	Only required if `rtn_pitch_opt = "probDist"`, a single row data frame with columns `mean` and `sd`, the mean and standard deviation of the blade pitch angle, i.e. the angle between the blade surface and the rotor plane, in degrees. Assumed to follow a tnorm-lw0 distribution.
`rtn_speed_pars`	Only required if `rtn_pitch_opt = "probDist"`, a single row data frame with columns `mean` and `sd`, the mean and standard deviation of the operational rotation speed, in revolutions per minute. Assumed to follow a tnorm-lw0 distribution.
`windspd_pars`	Only required if `rtn_pitch_opt = "windSpeedReltn"`, a single row data frame with columns `mean` and `sd`, the mean and the standard deviation of wind speed at the windfarm site, in metres/sec. Assumed to follow a tnorm-lw0 distribution.
`rtn_pitch_windspd_dt`	Only required if `rtn_pitch_opt = "windSpeedReltn"`, a data frame giving the relationship between wind speed, rotation speed and blade pitch values. It must contain the columns: `wind_speed`, wind speed in m/s, `rtn_speed`, rotation speed in rpm, `bld_pitch`, blade pitch values in degrees.
`trb_wind_avbl`	A data frame with the monthly estimates of operational wind availability. It must contain the columns: `month`, (unique) month names, `pctg`, the percentage of time wind conditions allow for turbine operation per month.
`trb_downtime_pars`	A data frame with monthly estimates of maintenance downtime, assumed to follow a tnorm-lw0 distribution. It must contain the following columns: `month`, (unique) month names, `mean`, numeric, the mean percentage of time in each month when turbines are not operating due to maintenance, `sd`, the standard deviation of monthly maintenance downtime.
`wf_n_trbs`	Integer, the number of turbines on the windfarm.
`wf_width`	Numeric value, the approximate longitudinal width of the wind farm, in kilometres (`w`).
`wf_latitude`	A decimal value. The latitude of the centroid of the windfarm, in degrees.
`tidal_offset`	A numeric value, the tidal offset, the difference between HAT and mean sea level, in metres.
`lrg_arr_corr`	Boolean value. If TRUE, the large array correction will be applied. This is a correction factor to account for the decay in bird density at later rows in wind farms with a large array of turbines.
`yinc`, `xinc`	numeric values, the increments along the y-axis and x-axis for numerical integration across segments of the rotor circle. Chosen values express proportion of rotor radius. By default these are set to 0.05, i.e. integration will be performed at a resolution of one twentieth of the rotor radius.
`out_format`	Output format specification. Possible values are: `"draws"`: returns stochastic draws of collisions estimates (default value), `"summaries"`: returns summary statistics of collisions estimates.
`out_sampled_pars`	Logical, whether to output summary statistics of values sampled for each stochastic model parameter.
`out_period`	Controls level of temporal aggregation of collision outputs. Possible values are: `"months"`: monthly collisions (default value), `"seasons"`: collisions per user-defined season, `"annum"`: total collisions over 12 months.
`season_specs`	Only required if `out_period = "seasons"`, a data frame defining the seasons for aggregating over collision estimates. It must comprise the following columns: `season_id`, (unique) season identifier, `start_month`, name of the season's first month, `end_month`, name of the season's last month.
`verbose`	Logical, print model run progress on the console?
`log_file`	Path to log file to store session info and main model run options. If set to NULL (default value), log file is not created.
`seed`	Integer, the random seed for random number generation, for analysis reproducibility.

Details

Collision risk can be calculated under 4 options, specified by model_options:

Option 1 - Basic model with proportion at collision risk height derived from site survey (prop_crh_surv).
Option 2 - Basic model with proportion at collision risk height derived from a generic flight height distribution (gen_fhd).
Option 3 - Extended model using a generic flight height distribution (gen_fhd).
Option 4 - Extended model using a site-specific flight height distribution (site_fhd).

Where,

Basic model - assumes a uniform distribution of bird flights at collision risk height (i.e. above the minimum and below the maximum height of the rotor blade).
Extended model - takes into account the distribution of bird flight heights at collision risk height.

Value

If out_sampled_pars = FALSE, returns a list with estimates of number of collisions per chosen time periods, with elements containing the outputs for each CRM Option.

If out_sampled_pars = TRUE, returns a list object with two top-level elements:

collisions, a list comprising collision estimates for each CRM Option,
sampled_pars, a list with summary statistics of values sampled for stochastic model parameters.

Examples

# ------------------------------------------------------
# Run with arbitrary parameter values, for illustration
# ------------------------------------------------------

# ------------------------------------------------------
# Setting some of the required inputs upfront
b_dens <- data.frame(
  month = month.abb,
  mean = runif(12, 0.8, 1.5),
  sd = runif(12, 0.2, 0.3)
)
head(b_dens)

# Generic FHD bootstraps from Johnson et al (2014)
fhd_boots <- generic_fhd_bootstraps[[1]]
head(fhd_boots)

# wind speed vs rotation speed vs blade pitch
wind_rtn_ptch <- data.frame(
  wind_speed = seq_len(30),
  rtn_speed = 10/(30:1),
  bld_pitch = c(rep(90, 4), rep(0, 8), 5:22)
)
head(wind_rtn_ptch)

# wind availability
windavb <- data.frame(
  month = month.abb,
  pctg = runif(12, 85, 98)
)
head(windavb)

# maintenance downtime
dwntm <- data.frame(
  month = month.abb,
  mean = runif(12, 6, 10),
  sd = rep(2, 12))
head(dwntm)

# seasons specification
seas_dt <- data.frame(
  season_id = c("a", "b", "c"),
  start_month = c("Jan", "May", "Oct"), end_month = c("Apr", "Sep", "Dec")
  )
head(seas_dt)

# ----------------------------------------------------------
# Run stochastic CRM, treating rotor radius, air gap and
# blade width as fixed parameters (i.e. not stochastic)

stoch_crm(
  model_options = c(1, 2, 3),
  n_iter = 1000,
  flt_speed_pars = data.frame(mean = 7.26, sd = 1.5),
  body_lt_pars = data.frame(mean = 0.39, sd = 0.005),
  wing_span_pars = data.frame(mean = 1.08, sd = 0.04),
  avoid_bsc_pars = data.frame(mean = 0.99, sd = 0.001),
  avoid_ext_pars = data.frame(mean = 0.96, sd = 0.002),
  noct_act_pars = data.frame(mean = 0.033, sd = 0.005),
  prop_crh_pars = data.frame(mean = 0.06, sd = 0.009),
  bird_dens_opt = "tnorm",
  bird_dens_dt = b_dens,
  flight_type = "flapping",
  prop_upwind = 0.5,
  gen_fhd_boots = fhd_boots,
  n_blades = 3,
  rtr_radius_pars = data.frame(mean = 80, sd = 0), # sd = 0, rotor radius is fixed
  air_gap_pars = data.frame(mean = 36, sd = 0),    # sd = 0, air gap is fixed
  bld_width_pars = data.frame(mean = 8, sd = 0),   # sd = 0, blade width is fixed
  rtn_pitch_opt = "windSpeedReltn",
  windspd_pars = data.frame(mean = 7.74, sd = 3),
  rtn_pitch_windspd_dt = wind_rtn_ptch,
  trb_wind_avbl = windavb,
  trb_downtime_pars = dwntm,
  wf_n_trbs = 200,
  wf_width = 15,
  wf_latitude = 56.9,
  tidal_offset = 2.5,
  lrg_arr_corr = TRUE,
  verbose = TRUE,
  seed = 1234,
  out_format = "summaries",
  out_sampled_pars = TRUE,
  out_period = "seasons",
  season_specs = seas_dt,
  log_file = NULL
)

[Package stochLAB version 1.1.2 Index]