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
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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'))

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:

61 exports 1 stars 0.75 score 74 dependencies 392 downloads

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

Target	Result	Date
Doc / Vignettes	OK	Aug 23 2024
R-4.5-win	NOTE	Aug 23 2024
R-4.5-linux	NOTE	Aug 23 2024
R-4.4-win	NOTE	Aug 23 2024
R-4.4-mac	NOTE	Aug 23 2024
R-4.3-win	NOTE	Aug 23 2024
R-4.3-mac	NOTE	Aug 23 2024

Exports:Acins addCarcass aic calcMstar cof2parms cofOK cofOK0 cofOKInf dd2ddSim ddCI ddd ddFit ddSim dmb dxep0 dxep012 dxep0123 dxep02 dxep1 dxep12 dxep123 dxep2 dxepi0 estdwp estpsi exclude exportGenEst fmmax fmmax.ab formatGenEst getncarc incGamma initLayout MCI modelFilter mpp2ddSim MpriorOK off parOK pdd pmb postM postM.ab prepmod prepRing psi_extend pxep0 pxep012 pxep0123 pxep02 pxep1 pxep12 pxep123 pxep2 pxepi0 qdd rcd rdd readCarcass rmat stats

Dependencies:base64enc boot bslib cachem class classInt cli commonmark cpp11 crayon crosstalk DBI digest DT e1071 evaluate expint fastmap fontawesome fs generics GenEst glue gsl gtools hellno highr htmltools htmlwidgets httpuv invgamma jquerylib jsonlite KernSmooth knitr later lattice lazyeval lifecycle lubridate magrittr MASS Matrix matrixStats memoise mime mvtnorm numDeriv plotrix pracma promises proxy R6 rappdirs Rcpp rlang rmarkdown s2 sass sf shiny shinyjs sourcetools statmod survival timechange tinytex units VGAM withr wk xfun xtable yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 Center	Acins
Add Carcasses to a Site Layout	addCarcass addCarcass.data.frame addCarcass.shapeCarcass
Calculate Akaike Information Criterion (AICc) for Distance Distributions	aic aic.dd aic.ddArray aic.ddArraycc
Names of the Named Distributions	alt_names
Example Carcass Distances to Accompany the Polygon Layout Data Set	carcass_polygon
Carcass Data to Accompany the Simple Geometry Data Format	carcass_simple
Full, Simulated carcass_simple Data Set (Including Locations and Missed Carcasses)	carcass_simple0
Names of the GLM Coefficients for Each Distribution	cof_name
Convert GLM Coefficients into Named Distribution Parameters	cof2parms cof2parms.dd cof2parms.matrix cof2parms.numeric parms2cof.matrix
Check Whether GLM Coefficients Give Proper Distribution	cofOK cofOK0 cofOKInf
Constraints on GLM Coefficients for Extensibility to a Distribution	constraints
Constraints on Parameters to Assure Extensibility	constraints_par
Extract Parameters from a Distance Model ('dd') and Format as 'ddSim' Object	dd2ddSim
Calculate CI for CDF, PDF, or quantile	ddCI
Calculate Probability Functions for Distance Distributions	ddd 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' Package	ddPrint print.dd print.ddArray print.fmod
Simulation of Dispersion Parameters	ddSim ddSim.dd
An Ordering of the Models by Degree of the Polynomial	degOrder
Full List of Names of Distributions	distr_names
Probability Distributions for Carcasses Versus Distance from Turbine	Distributions dmb dxep0 dxep012 dxep0123 dxep02 dxep1 dxep12 dxep123 dxep2 dxepi0 pmb pxep0 pxep012 pxep0123 pxep02 pxep1 pxep12 pxep123 pxep2 pxepi0
Density-Weighted Proportion	dwp
Estimate DWP	estdwp estdwp.psiHat estdwp.psiHatcc
Estimate Probability Carcass lands in Searched Area	estpsi estpsi.data.frame estpsi.rdat estpsi.rings estpsi.ringscc estpsi.rpA estpsi.xyLayout
Remove Particular Names from a Longer List	exclude
Export Estimated Density-Weighted Proportion to File in Proper GenEst Format	exportGenEst
Find suitable mmax for clipping improper priors for M	fmmax fmmax.ab
Format DWP Estimate for Use in GenEst	formatGenEst
Simple Function to Extract Carcass Counts	getncarc getncarc.dd getncarc.ddArray getncarc.ddArraycc getncarc.rings getncarc.ringscc getncarc.xyLayout
Incomplete Gamma Function	incGamma
Create a Data Structure or Map for the Site Layout	initLayout
Example Bare Vector Format for Eagle Data	layout_eagle
Example Polygon Data for Site Layout	layout_polygon
Example Simple Geometry Data Format for Site Layout	layout_simple
Example Data for Site Layout on an (x, y) Grid	layout_xy
Names of All the Available Models	mod_all
Vector of Colors Used in Graphs of Fitted Models	mod_color
Vector of Line Types Used in Graphs of Fitted Models	mod_lty
Vector of GLM Offsets for Available Models	mod_offset
Vector of Names of Standard Models	mod_standard
Vector of Names of Models Available for Grid Layout	mod_xy
Run Models through a Sieve to Filter out Dubious Fits	modelFilter
Convert Distribution Name + Parameters to 'ddSim' Object	mpp2ddSim
Check validity of format of custom prior for M	MpriorOK
Vector of Names of Models with Natural Offset	natural
Utility Function for Constructing Offsets for GLMs	off
Default Graphics Parameters	par_default
List of Names of the Distribution Parameters Associated with Respective Models	parm_name
Check Parameter Value Validity the Distribution	parOK
Plot dd and ddArray Objects	Plot 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 Psihat	prepmod
Format a Search Layout into Rings for Analysis	prepRing prepRing.numeric prepRing.polygonLayout prepRing.shapeLayout prepRing.simpleLayout
Simple Extension of a 'dd' Model beyond the Search Radius	psi_extend
Import Carcass Observations Locations from Shape Files	readCarcass
Simple Utility Function Used in Optimizing the GLM	rmat
Test Criteria for Model Selection	sieve_default
Test Criteria for Model Selection within Search Area	sieve_win
Display a Tables of Summary Statistics for Distance Distributions	stats stats.dd stats.ddArray stats.ddArraycc
Subset Data from an Imported and Formatted Shape File	subset.shapeCarcass subset.shapeLayout
Locations of All Carcasses in Grid Data	xyr