Package: dwp 1.1

dwp: Density-Weighted Proportion

Fit a Poisson regression to carcass distance data and integrate over the searched area at a wind farm to estimate the fraction of carcasses falling in the searched area and format the output for use as the dwp parameter in the 'GenEst' or 'eoa' package for estimating bird and bat mortality, following Dalthorp, et al. (2022) <arxiv:2201.10064>.

Authors:Daniel Dalthorp [aut, cre], Manuela Huso [aut]

dwp_1.1.tar.gz
dwp_1.1.zip(r-4.5)dwp_1.1.zip(r-4.4)dwp_1.1.zip(r-4.3)
dwp_1.1.tgz(r-4.4-any)dwp_1.1.tgz(r-4.3-any)
dwp_1.1.tar.gz(r-4.5-noble)dwp_1.1.tar.gz(r-4.4-noble)
dwp_1.1.tgz(r-4.4-emscripten)dwp_1.1.tgz(r-4.3-emscripten)
dwp.pdf |dwp.html✨
dwp/json (API)

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

Peer review:

Bug tracker:https://github.com/ddalthorp/dwp/issues

Datasets:
  • alt_names - Names of the Named Distributions
  • carcass_polygon - Example Carcass Distances to Accompany the Polygon Layout Data Set
  • carcass_simple - Carcass Data to Accompany the Simple Geometry Data Format
  • carcass_simple0 - Full, Simulated carcass_simple Data Set
  • cof_name - Names of the GLM Coefficients for Each Distribution
  • constraints - Constraints on GLM Coefficients for Extensibility to a Distribution
  • constraints_par - Constraints on Parameters to Assure Extensibility
  • degOrder - An Ordering of the Models by Degree of the Polynomial
  • distr_names - Full List of Names of Distributions
  • layout_eagle - Example Bare Vector Format for Eagle Data
  • layout_polygon - Example Polygon Data for Site Layout
  • layout_simple - Example Simple Geometry Data Format for Site Layout
  • layout_xy - Example Data for Site Layout on an (x, y) Grid
  • mod_all - Names of All the Available Models
  • mod_color - Vector of Colors Used in Graphs of Fitted Models
  • mod_lty - Vector of Line Types Used in Graphs of Fitted Models
  • mod_offset - Vector of GLM Offsets for Available Models
  • mod_standard - Vector of Names of Standard Models
  • mod_xy - Vector of Names of Models Available for Grid Layout
  • natural - Vector of Names of Models with Natural Offset
  • par_default - Default Graphics Parameters
  • parm_name - List of Names of the Distribution Parameters Associated with Respective Models
  • sieve_default - Test Criteria for Model Selection
  • sieve_win - Test Criteria for Model Selection within Search Area
  • xyr - Locations of All Carcasses in Grid Data

On CRAN:

2.70 score 1 stars 248 downloads 61 exports 74 dependencies

Last updated 1 years agofrom:c3ef6e14d0. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winNOTENov 21 2024
R-4.5-linuxNOTENov 21 2024
R-4.4-winNOTENov 21 2024
R-4.4-macNOTENov 21 2024
R-4.3-winNOTENov 21 2024
R-4.3-macNOTENov 21 2024

Exports:AcinsaddCarcassaiccalcMstarcof2parmscofOKcofOK0cofOKInfdd2ddSimddCIdddddFitddSimdmbdxep0dxep012dxep0123dxep02dxep1dxep12dxep123dxep2dxepi0estdwpestpsiexcludeexportGenEstfmmaxfmmax.abformatGenEstgetncarcincGammainitLayoutMCImodelFiltermpp2ddSimMpriorOKoffparOKpddpmbpostMpostM.abprepmodprepRingpsi_extendpxep0pxep012pxep0123pxep02pxep1pxep12pxep123pxep2pxepi0qddrcdrddreadCarcassrmatstats

Dependencies:base64encbootbslibcachemclassclassIntclicommonmarkcpp11crayoncrosstalkDBIdigestDTe1071evaluateexpintfastmapfontawesomefsgenericsGenEstgluegslgtoolshellnohighrhtmltoolshtmlwidgetshttpuvinvgammajquerylibjsonliteKernSmoothknitrlaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmatrixStatsmemoisemimemvtnormnumDerivplotrixpracmapromisesproxyR6rappdirsRcpprlangrmarkdowns2sasssfshinyshinyjssourcetoolsstatmodsurvivaltimechangetinytexunitsVGAMwithrwkxfunxtableyaml

Readme and manuals

Help Manual

Help pageTopics
Subset a Set of Fitted Dispersion Models ('ddArray')[.ddArray
Subset Simulated Dispersion Parameters while Preserving Attributes[.ddSim
Calculate Area of Intersection inside Circle and Square with Common CenterAcins
Add Carcasses to a Site LayoutaddCarcass addCarcass.data.frame addCarcass.shapeCarcass
Calculate Akaike Information Criterion (AICc) for Distance Distributionsaic aic.dd aic.ddArray aic.ddArraycc
Names of the Named Distributionsalt_names
Example Carcass Distances to Accompany the Polygon Layout Data Setcarcass_polygon
Carcass Data to Accompany the Simple Geometry Data Formatcarcass_simple
Full, Simulated carcass_simple Data Set (Including Locations and Missed Carcasses)carcass_simple0
Names of the GLM Coefficients for Each Distributioncof_name
Convert GLM Coefficients into Named Distribution Parameterscof2parms cof2parms.dd cof2parms.matrix cof2parms.numeric parms2cof.matrix
Check Whether GLM Coefficients Give Proper DistributioncofOK cofOK0 cofOKInf
Constraints on GLM Coefficients for Extensibility to a Distributionconstraints
Constraints on Parameters to Assure Extensibilityconstraints_par
Extract Parameters from a Distance Model ('dd') and Format as 'ddSim' Objectdd2ddSim
Calculate CI for CDF, PDF, or quantileddCI
Calculate Probability Functions for Distance Distributionsddd pdd qdd rcd rdd
Fit Distance Distribution Model(s)ddFit ddFit.data.frame ddFit.list ddFit.rings ddFit.ringscc ddFit.xyLayout
Print S3 Objects in 'dwp' PackageddPrint print.dd print.ddArray print.fmod
Simulation of Dispersion ParametersddSim ddSim.dd
An Ordering of the Models by Degree of the PolynomialdegOrder
Full List of Names of Distributionsdistr_names
Probability Distributions for Carcasses Versus Distance from TurbineDistributions dmb dxep0 dxep012 dxep0123 dxep02 dxep1 dxep12 dxep123 dxep2 dxepi0 pmb pxep0 pxep012 pxep0123 pxep02 pxep1 pxep12 pxep123 pxep2 pxepi0
Density-Weighted Proportiondwp
Estimate DWPestdwp estdwp.psiHat estdwp.psiHatcc
Estimate Probability Carcass lands in Searched Areaestpsi estpsi.data.frame estpsi.rdat estpsi.rings estpsi.ringscc estpsi.rpA estpsi.xyLayout
Remove Particular Names from a Longer Listexclude
Export Estimated Density-Weighted Proportion to File in Proper GenEst FormatexportGenEst
Find suitable mmax for clipping improper priors for Mfmmax fmmax.ab
Format DWP Estimate for Use in GenEstformatGenEst
Simple Function to Extract Carcass Countsgetncarc getncarc.dd getncarc.ddArray getncarc.ddArraycc getncarc.rings getncarc.ringscc getncarc.xyLayout
Incomplete Gamma FunctionincGamma
Create a Data Structure or Map for the Site LayoutinitLayout
Example Bare Vector Format for Eagle Datalayout_eagle
Example Polygon Data for Site Layoutlayout_polygon
Example Simple Geometry Data Format for Site Layoutlayout_simple
Example Data for Site Layout on an (x, y) Gridlayout_xy
Names of All the Available Modelsmod_all
Vector of Colors Used in Graphs of Fitted Modelsmod_color
Vector of Line Types Used in Graphs of Fitted Modelsmod_lty
Vector of GLM Offsets for Available Modelsmod_offset
Vector of Names of Standard Modelsmod_standard
Vector of Names of Models Available for Grid Layoutmod_xy
Run Models through a Sieve to Filter out Dubious FitsmodelFilter
Convert Distribution Name + Parameters to 'ddSim' Objectmpp2ddSim
Check validity of format of custom prior for MMpriorOK
Vector of Names of Models with Natural Offsetnatural
Utility Function for Constructing Offsets for GLMsoff
Default Graphics Parameterspar_default
List of Names of the Distribution Parameters Associated with Respective Modelsparm_name
Check Parameter Value Validity the DistributionparOK
Plot dd and ddArray ObjectsPlot plot.dd plot.ddArray plot.dwphat plot.fmod plot.layoutSimple plot.polygonLayout plot.psiHat
Calculate posterior distribution of M and extract statistics (M* and CI)calcMstar MCI postM postM.ab
Internal Utility Function to Parse and Format Model for Calculating Psihatprepmod
Format a Search Layout into Rings for AnalysisprepRing prepRing.numeric prepRing.polygonLayout prepRing.shapeLayout prepRing.simpleLayout
Simple Extension of a 'dd' Model beyond the Search Radiuspsi_extend
Import Carcass Observations Locations from Shape FilesreadCarcass
Simple Utility Function Used in Optimizing the GLMrmat
Test Criteria for Model Selectionsieve_default
Test Criteria for Model Selection within Search Areasieve_win
Display a Tables of Summary Statistics for Distance Distributionsstats stats.dd stats.ddArray stats.ddArraycc
Subset Data from an Imported and Formatted Shape Filesubset.shapeCarcass subset.shapeLayout
Locations of All Carcasses in Grid Dataxyr