Package: stochLAB 1.1.2

Grant Humphries

stochLAB: Stochastic Collision Risk Model

Collision Risk Models for avian fauna (seabird and migratory birds) at offshore wind farms. The base deterministic model is derived from Band (2012) <https://tethys.pnnl.gov/publications/using-collision-risk-model-assess-bird-collision-risks-offshore-wind-farms>. This was further expanded on by Masden (2015) <doi:10.7489/1659-1> and code used here is heavily derived from this work with input from Dr A. Cook at the British Trust for Ornithology. These collision risk models are useful for marine ornithologists who are working in the offshore wind industry, particularly in UK waters. However, many of the species included in the stochastic collision risk models (stoch_crm) can also be found in the North Atlantic in the United States and Canada, and could be applied there.

Authors:Grant Humphries [aut, cre], Bruno Caneco [aut], Aonghais Cook [aut], Elizabeth Masden [aut], Marine Scotland [fnd, cph], HiDef [cph], DMPstats [cph], Kelly Street [rev]

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stochLAB.pdf |stochLAB.html
stochLAB/json (API)
NEWS

# Install 'stochLAB' in R:
install.packages('stochLAB', repos = c('https://hidef-aerial-surveying.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/hidef-aerial-surveying/stochlab/issues

Datasets:

On CRAN:

collision-riskmigratoryspeciesoffshore-windseabirds

4.78 score 6 stars 10 scripts 161 downloads 32 exports 30 dependencies

Last updated 2 years agofrom:8fd8136da5. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:%>%band_crmcrm_opt1crm_opt2crm_opt3crm_opt4Day_Lengthformat_monthsgenerate_rotor_gridsget_avg_prob_collisionget_collisions_basicget_collisions_extendedget_fhd_rotorget_flux_factorget_lac_factorget_mig_flux_factorget_pcoll_gridget_phi_gridget_prop_crh_fhdget_risk_yget_x_gridget_y_gridmig_stoch_crmrbeta_dmprtnorm_dmpsample_parameterssample_qtlssample_turbine_mCRMsampler_hdseq_monthsstoch_crmvalidate_inputs

Dependencies:clicommoncpp11dplyrexpmfansigenericsgluelatticelifecyclelogrmagrittrMatrixmsmmvtnormpillarpkgconfigpracmapurrrR6rlangstringistringrsurvivaltibbletidyrtidyselectutf8vctrswithr

Running stochLAB

Rendered fromRunning_stochLAB.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-12-21
Started: 2022-02-24

Readme and manuals

Help Manual

Help pageTopics
Collision risk model, for a single species and one turbine scenarioband_crm
Parameter values and outputs from Band's Collision Risk spreadsheet ("Final_Report_SOSS02_BandSpreadSheetWorkedExampl1.xlsm")band_spreadsheet_dt
Parameter values and outputs from Band's Collision Risk spreadsheet, example nr. 2band_spreadsheet_dt_2
Example of bird parameters stored in wide formatbird_pars_wide_example
Rotor blade chord profilechord_prof_5MW
Number of collisions under model option 1crm_opt1
Number of collisions under model option 2crm_opt2
Number of collisions under model Option 3crm_opt3
Number of collisions under model Option 4crm_opt4
Total day and night hours per monthDay_Length
Example of Truncated Normal parameters for monthly estimates of bird densitydens_tnorm_wide_example
Format any month name to three letter codeformat_months
Geometric attributes at equidistant points within the rotor's unit circlegenerate_rotor_grids
Bootstrap samples of generic FHDs of 25 seabird speciesgeneric_fhd_bootstraps
Average single transit collision risk with no avoidanceget_avg_prob_collision
Get expected collisions based on the basic modelget_collisions_basic
Number of collisions based on the extended modelget_collisions_extended
Returns the proportion of birds at height bands along the rotorget_fhd_rotor
Flux factorget_flux_factor
Large array correction factorget_lac_factor
Migration Flux factorget_mig_flux_factor
Grid of probabilities of single transit collision at points in rotor circleget_pcoll_grid
Grid with angles between points (x, y) and the rotor's vertical axisget_phi_grid
Calculate the total proportion of bird flights at collision risk based on a flight height distributionget_prop_crh_fhd
Single transit collision risk along the chord of the rotor at height band yget_risk_y
Grid of horizontal distances from points in the rotor circle to its vertical axisget_x_grid
Grid of vertical distances from points in the rotor circle to its horizontal axisget_y_grid
Summarized flight height profiles from Johnston et al (2014)Johnston_Flight_heights_SOSS
Stochastic migration collision risk modelmig_stoch_crm
Customised sampling functions for the Beta distributionsrbeta_dmp
Sample rotor grids for generated_rotor_grids unit testrotor_grids_test
Customised sampling of Truncated Normal distributionrtnorm_dmp
Parameter sampling whizsample_parameters
Generate random draws based on empirical c.d.f.sample_qtls
Sampling function for a single turbine in the mCRMsample_turbine_mCRM
Customised sampling function wrappersampler_hd
Generate sequence of monthsseq_months
Stochastic collision risk model for a single species and one wind farm scenariostoch_crm
stochLAB: Stochastic Collision Risk ModelstochLAB
Example of turbine and windfarm parameters stored in wide formatturb_pars_wide_example
Input validatorvalidate_inputs
Example of data with relationship between wind speed, rotation speed and blade pitchwndspd_rtn_ptch_example