R/data.R
In ddalthorp/GenEst: Generalized Mortality Estimator
# Mock ------------------------------
#' A mock example data set
#'
#' A template dataset used for testing purposes. Dataset containing SE, CP, SS,
#' DWP, and CO data. Data are mostly random without patterns.
#'
#' @format A list with 5 items:
#' \describe{
#' \item{SE}{Searcher efficiency trial data}
#' \item{CP}{Carcass persistence trial data}
#' \item{SS}{Search schedule data}
#' \item{DWP}{Density weighted proportion of area searched data}
#' \item{CO}{Carcass observations}
#' }
#' @source \code{mock}
"mock"
# Cleared ------------------------------
#' Wind cleared plot (60m) Search Example
#'
#' A complete example data set for estimating fatalities from 60 m cleared plots
#' at 23 out of 100 searches at a wind power facility. Data on carcass
#' observations (CO) from a search of all terrain out to 60m from each of 100
#' turbines at a theoretical site, field trials for estimating carcass
#' persistence (CP) and searcher efficiency (SE), search schedule (SS)
#' parameters (for example, which turbines were searched on which days), and
#' density weighted proportion (DWP) of area searched at each turbine (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{wind_cleared} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#'
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{pkID}}{unique ID for each carcass}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{Visibility}}{indicator for visibility class of the ground, with
#' \code{"RP"} for carcasses placed on a road or turbine pad, \code{"M"}
#' for moderate visibility (e.g., plowed field; short, sparse vegetation),
#' or \code{"D"} for difficult visibility}
#' \item{\code{"s1",...,"s5"}}{fate of carcass on the 1st, 2nd, 3rd, 4th, and
#' 5th search after placement. A value of 1 implies that a carcass was
#' discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "SN" could be used to indicate that the
#' turbine was not searched because of snow, or "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' }
#'
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{cpID}}{unique ID for each carcass}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{Visibility}}{indicator for visibility class of the ground, with
#' \code{"RP"} for carcasses placed on a road or turbine pad, \code{"M"} for
#' moderate visibility (e.g., plowed field; short, sparse vegetation), or
#' \code{"D"} for difficult visibility.} \item{\code{LastPresent},
#' \code{FirstAbsent}}{endpoints of the interval bracketing the time the carcass
#' was scavenged or otherwise removed from the field. For example,
#' \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the carcass was
#' last observed 2.04 days after being placed in the field and was noted
#' missing 3.21 days after being placed. If the precise time of carcass
#' removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date a turbine at the site
#' was searched, a column of \code{SearchDate}s, and a column for each turbine.
#' In addition, there is a column to indicate the \code{Season}. A column with
#' search dates and columns for each turbine searched are required. Other
#' columns are optional.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates on which at least one turbine was
#' searched. Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone
#' (\code{CDT}) is optional. A time stamp may be included if desired (e.g.,
#' \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used in place
#' of \code{-}.}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"} to
#' indicate which season the search was conducted in. \code{Season} is
#' optional but may be used as a temporal covariate for fatality estimates.}
#' \item{\code{t1}, etc.}{unique ID for all turbines that were searched on at
#' least one search date. Values are either 1 or 0, indicating whether the
#' given turbine (column) was searched or not on the given date (row).}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each turbine and columns for
#' each carcass size class. Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area).
#' \describe{
#' \item{\code{Turbine}}{unique ID for each turbine. IDs match those used in
#' the \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{Size}}{\code{bat}, \code{sml}, \code{med}, \code{lrg}}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"} to
#' indicate which season the search was conducted in. \code{Season} is
#' optional but may be used as a temporal covariate for fatality estimates.}}
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given carcass
#' (date found, size, species, etc.)
#' \describe{
#' \item{\code{carcID}}{unique identifier for each carcass: \code{"x30"},
#' \code{"x46"}, etc.}
#' \item{\code{Turbine}}{identifier for which turbine the given carcass was
#' found at: \code{"t19"}, \code{"t65"}, \code{"t49"}, etc.}
#' \item{\code{TurbineType}}{the type of turbine: \code{"X"}, \code{"Y"} or
#' \code{"Z"}. }
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included
#' in the search schedule (\code{$SS$SearchDate})}
#' \item{\code{Visibility}}{visibility class: \code{"RP"}, \code{"M"}, or
#' \code{"D"}, as described in \code{$CP} and \code{$SE}}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{SpeciesGroup}}{species group: \code{"bat0"}, \code{"bat1"},
#' \code{"brd1"}, \code{"brd2"}, \code{"brd3"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Distance}}{distance from the turbine}
#' }
#'
#' @source \code{wind_cleared}
"wind_cleared"
# RP ------------------------------
#' Wind Road and Pad (120m) Example
#'
#' This example dataset is based on 120 m radius road and pad searches of all
#' 100 turbines at a theoretical site. The simulated site consists of 100
#' turbines, searched on roads and pads only, out to 120 meters. Search
#' schedule differs by turbine and season, with more frequent searches in the
#' fall, and a subset of twenty turbines searched at every scheduled search.
#'
#' Data on carcass observations (CO) from searches, field trials for estimating
#' carcass persistence (CP) and searcher efficiency (SE), search schedule (SS)
#' parameters (for example, which turbines were searched on which days), and
#' density weighted proportion (DWP) of area searched at each turbine (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{wind_RP} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#'
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{pkID}}{unique ID for each carcass}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{"s1",...,"s5"}}{fate of carcass on the 1st, 2nd, 3rd, 4th, and
#' 5th search after placement. A value of 1 implies that a carcass was
#' discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "SN" could be used to indicate that the
#' turbine was not searched because of snow, or "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{cpID}}{unique ID for each carcass}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird.}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing the
#' time the carcass was scavenged or otherwise removed from the field. For
#' example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the carcass
#' was last observed 2.04 days after being placed in the field and was noted
#' missing 3.21 days after being placed. If the precise time of carcass
#' removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date a turbine at the site
#' was searched, a column of \code{SearchDate}s, and a column for each turbine.
#' In addition, there is a column to indicate the \code{Season}. A column with
#' search dates and columns for each turbine searched are required. Other
#' columns are optional.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates on which at least one turbine was
#' searched. Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone
#' (\code{CDT}) is optional. A time stamp may be included if desired
#' (e.g., \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used
#' in place of \code{-}.}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"} to
#' indicate which season the search was conducted in. \code{Season} is
#' optional but may be used as a temporal covariate for fatality estimates.}
#' \item{\code{t1}, etc.}{unique ID for all turbines that were searched on at
#' least one search date. Values are either 1 or 0, indicating whether the
#' given turbine (column) was searched or not on the given date (row).}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each turbine and columns for
#' each carcass size class. Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area).
#' \describe{
#' \item{\code{Turbine}}{unique ID for each turbine. IDs match those used in
#' the \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{DWP associated with size class Bat.}
#' \item{\code{sml}}{DWP associated with size class Small.}
#' \item{\code{med}}{DWP associated with size class Medium.}
#' \item{\code{lrg}}{DWP associated with size class Large.}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given
#' carcass (date found, size, species, etc.)
#' \describe{
#' \item{\code{carcID}}{unique identifier for each carcass: \code{"x30"},
#' \code{"x46"}, etc.}
#' \item{\code{Turbine}}{identifier for which turbine the given carcass was
#' found at: \code{"t19"}, \code{"t65"}, \code{"t49"}, etc.}
#' \item{\code{TurbineType}}{the type of turbine: \code{"X"}, \code{"Y"} or
#' \code{"Z"}. }
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included
#' in the search schedule (\code{$SS$SearchDate}}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{SpeciesGroup}}{species group: \code{"bat0"}, \code{"bat1"},
#' \code{"brd1"}, \code{"brd2"}, \code{"brd3"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Distance}}{distance from the turbine}
#' }
#'
#' @source \code{wind_RP}
"wind_RP"
# RPbat ------------------------------
#' Wind Bat-Only Road and Pad (120m) Example
#'
#' This example dataset considers only bats found on 120 m radius road and pad
#' searches of all 100 turbines at a theoretical site. The simulated site
#' consists of 100 turbines, searched on roads and pads only, out to 120
#' meters. Search schedule differs by turbine and season, with more frequent
#' searches in the fall, and a subset of twenty turbines searched at every
#' scheduled search.
#'
#' Data on carcass observations (CO) from searches, field trials for estimating
#' carcass persistence (CP) and searcher efficiency (SE), search schedule (SS)
#' parameters (for example, which turbines were searched on which days), and
#' density weighted proportion (DWP) of area searched at each turbine (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{wind_RPbat} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#'
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{pkID}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{"s1",...,"s5"}}{fate of carcass on the 1st, 2nd, 3rd, 4th, and
#' 5th search after placement. A value of 1 implies that a carcass was
#' discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "SN" could be used to indicate that the
#' turbine was not searched because of snow, or "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{cpID}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing
#' the time the carcass was scavenged or otherwise removed from the field.
#' For example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the
#' carcass was last observed 2.04 days after being placed in the field and
#' was noted missing 3.21 days after being placed. If the precise time of
#' carcass removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date a turbine at the site
#' was searched, a column of \code{SearchDate}s, and a column for each turbine.
#' In addition, there is a column to indicate the \code{Season}. A column with
#' search dates and columns for each turbine searched are required. Other
#' columns are optional.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates on which at least one turbine was
#' searched. Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone
#' (\code{CDT}) is optional. A time stamp may be included if desired
#' (e.g., \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used
#' in place of \code{-}.}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"} to
#' indicate which season the search was conducted in. \code{Season} is
#' optional but may be used as a temporal covariate for fatality estimates.}
#' \item{\code{t1}, etc.}{unique ID for all turbines that were searched on at
#' least one search date. Values are either 1 or 0, indicating whether the
#' given turbine (column) was searched or not on the given date (row).}
#' }
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each turbine and columns for
#' each carcass size class. Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area).
#' \describe{
#' \item{\code{Turbine}}{unique ID for each turbine. IDs match those used in
#' the \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{Contains the DWP for each turbine, with respect to size
#' class (in this case, bats only.}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given
#' carcass (date found, size, species, etc.)
#' \describe{
#' \item{\code{carcID}}{unique identifier for each carcass: \code{"x30"},
#' \code{"x46"}, etc.}
#' \item{\code{Turbine}}{identifier for which turbine the given carcass was
#' found at: \code{"t19"}, \code{"t65"}, \code{"t49"}, etc.}
#' \item{\code{TurbineType}}{the type of turbine: \code{"X"}, \code{"Y"} or
#' \code{"Z"}. }
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included
#' in the search schedule (\code{$SS$SearchDate}}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{SpeciesGroup}}{species group: \code{"bat0"}, \code{"bat1"},
#' \code{"brd1"}, \code{"brd2"}, \code{"brd3"}}
#' \item{\code{Distance}}{Distance from the turbine.}
#' }
#' @source \code{wind_RPbat}
"wind_RPbat"
# Trough ------------------------------
#' Trough-based solar thermal power simulated example
#'
#' An example data set for estimating fatalities from a trough-based solar
#' thermal electric power generation facility. The simulated site is inspected
#' daily along ten 2000 meter long transects, which run north-south. Observers
#' look up to 150 meters away down the rows created by troughs (east-west).
#' One sided distance sampling will be used, with observers looking consistently
#' in one cardinal direction as they travel through the facility. A sitewide
#' clearout search is implemented before the first scheduled winter search.
#'
#' The dataset consists of five parts: Data on carcass observations (CO) from
#' daily searches, field trials for estimating carcass persistence (CP) and
#' searcher efficiency (SE), search schedule (SS), and density weighted
#' proportion (DWP) of area searched for the rows within each transect (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{solar_trough} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{"Search1",...,"Search5"}}{fate of carcass on the 1st, 2nd, 3rd,
#' 4th, and 5th search after placement. A value of 1 implies that a carcass
#' was discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' \item{\code{Distance}}{the distance a carcass was placed from the
#' observer's transect.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{Index}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing the
#' time the carcass was scavenged or otherwise removed from the field. For
#' example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the carcass
#' was last observed 2.04 days after being placed in the field and was noted
#' missing 3.21 days after being placed. If the precise time of carcass
#' removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it was
#' observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date a transect at the site
#' was searched, a column of \code{SearchDate}s, and a column for each
#' transect. In addition, there is an optional column to indicate the
#' \code{Season}. The columns for distinct area (array) and the date column
#' are required, and the names of the columns for search areas must match the
#' names of areas used in the DWP and CO files.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates when a transect was searched.
#' Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone (\code{CDT})
#' is optional. A time stamp may be included if desired (e.g.,
#' \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used in
#' place of \code{-}.}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"} to indicate which season the search was conducted in.
#' \code{Season} is optional but may be used as a temporal covariate for
#' fatality estimates.}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each transect and columns for
#' each carcass size class (labels must match those of the class factors in the
#' carcass observation file). Values represent the density-weighted proportion
#' of the searched area for each size (or the fractionof carcasses that fall
#' in the searched area). Since the whole site was searched, DWP is uniformly
#' set equal to 1.
#' \describe{
#' \item{\code{Unit}}{unique ID for each transect. IDs match those used in
#' the \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{DWP associated with size class Bat}
#' \item{\code{sml}}{DWP associated with size class Small}
#' \item{\code{med}}{DWP associated with size class Medium}
#' \item{\code{lrg}}{DWP associated with size class Large}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given carcass
#' (date found, size, species, etc.)
#' \describe{
#' \item{\code{Index}}{unique identifier for each carcass.}
#' \item{\code{Unit}}{identifier for which transect the given carcass was
#' found at. Values must match with DWP Transect values Search Schedule
#' column names.}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Row}}{Optional indicator of which row within an array a carcass
#' was found at.}
#' \item{\code{Distance}}{The perpendicular distance from the searcher's
#' transect at which the carcass was discovered at.}
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}.
#' Every date entered here is (and must be) included in the search schedule
#' (\code{$SS$SearchDate})}
#' \item{\code{X}}{UTM Easting of carcass.}
#' \item{\code{Y}}{UTM Northing of carcass.}
#' }
#'
#' @source \code{solar_trough}
"solar_trough"
# PV ------------------------------
#' Photovoltaic Example Dataset
#'
#' An example data set for estimating fatalities from a large photovoltaic solar
#' generation facility.
#'
#' The simulated site is organized into 300 arrays of panels. As observers walk
#' north-south along paths between arrays, they look east or west down rows
#' between solar panels 150 meters long, with 38 searchable rows per array.
#' Observers consistently look for animals down one cardinal direction, making
#' this a one-sided distance sample. Searches are scheduled on a seven day
#' rotation, with 60 arrays searched per weekday. A sitewide clearout search
#' is implemented before the first scheduled winter search.
#'
#' The dataset consists of five parts: Data on carcass observations (CO) from
#' array searches, field trials for estimating carcass persistence (CP) and
#' searcher efficiency (SE), search schedule (SS), and density weighted
#' proportion (DWP) of area searched at each array (which is an area adjustment
#' factor to account for incomplete search coverage).
#'
#' @format \code{solar_PV} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{"Search1",...,"Search5"}}{fate of carcass on the 1st, 2nd, 3rd,
#' 4th, and 5th search after placement. A value of 1 implies that a carcass
#' was discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' \item{\code{Distance}}{the distance a carcass was placed from the
#' observer's transect. Used in determining probability to detect with
#' distance sampling.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{Index}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing
#' the time the carcass was scavenged or otherwise removed from the field.
#' For example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the
#' carcass was last observed 2.04 days after being placed in the field and
#' was noted missing 3.21 days after being placed. If the precise time of
#' carcass removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date an array at the site was
#' searched, a column of \code{SearchDate}s, and a column for each array. In
#' addition, there is an optional column to indicate the \code{Season}. The
#' columns for distinct area (array) and the date column are required, and the
#' names of the columns for search areas must match the names of areas used in
#' the DWP and CO files.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates when arrays were searched. Format
#' in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone (\code{CDT}) is
#' optional. A time stamp may be included if desired (e.g.,
#' \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used in
#' place of \code{-}.}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"},
#' or \code{"fall"} to indicate which season the search was conducted in.
#' \code{Season} is optional but may be used as a temporal covariate for
#' fatality estimates.}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each array and columns for each
#' carcass size class (labels must match those of the class factors in the
#' carcass observation file). Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area). In this example, observers walk along transects
#' separated by 150 meters, and search coverage is assumed to be 100%, i.e.,
#' DWP = 1 for each unit. This requires that carcasses be placed at random
#' locations in the field, even at distances from the transects that would make
#' it unlikely to observe small carcasses.
#' \describe{
#' \item{\code{Unit}}{unique ID for each array. IDs match those used in the
#' \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{DWP associated with size class Bat}
#' \item{\code{sml}}{DWP associated with size class Small}
#' \item{\code{med}}{DWP associated with size class Medium}
#' \item{\code{lrg}}{DWP associated with size class Large}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given
#' carcass (date found, size, species, etc.)
#' \describe{
#' \item{\code{Index}}{unique identifier for each carcass.}
#' \item{\code{Unit}}{identifier for which unit the given carcass was found
#' at: \code{"arc19"}, \code{"arc65"}, etc, for arcs in the outer heliostat
#' field, or \code{"center"}, indicating the inner heliostat field.}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Row}}{Optional indicator of which row within an array a carcass
#' was found at.}
#' \item{\code{Distance}}{The perpendicular distance from the searcher's
#' transect at which the carcass was discovered at.}
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included in
#' the search schedule
#' (\code{$SS$SearchDate}}
#' \item{\code{X}}{UTM Easting of carcass.}
#' \item{\code{Y}}{UTM Northing of carcass.}
#' }
#'
#' @source \code{solar_PV}
"solar_PV"
# Power Tower ------------------------------
#' Power Tower Example Dataset
#'
#' An example data set for estimating fatalities from a concentrating
#' solar-thermal (power tower) generation facility.
#'
#' The simulated site consists of a single tower generating approximately 130
#' MW. The tower is surrounded by a 250 meter radius circular inner field of
#' heliostats, searched on a weekly schedule. From the inner circle, 18
#' concentric rings of heliostats 50 meters deep extend to the boundaries of the
#' simulated site. Rings are subdivided into 8 arcs each, with arcs 1-8
#' immediately adjacent to the central circle. Arcs are search using distance
#' sampling techniques on a weekly schedule, with 29 arcs searched per weekday.
#'
#' There are two sources of mortality simulated: flux and non-flux (collision or
#' unknown cause).Flux carcasses are generated (weibull) about the tower, with
#' 5\% to be found in the outer field. Non-flux mortality is assumed uniform
#' across the site.
#'
#' The dataset consists of five parts: Data on carcass observations (CO) from
#' inner and outer heliostat searches, field trials for estimating carcass
#' persistence (CP) and searcher efficiency (SE), search schedule (SS), and
#' density weighted proportion (DWP) of area searched at each turbine (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{solar_powerTower} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{Field}}{indicates carcass placed in inner or outer heliostat
#' field, with levels \code{"inner"} or \code{outer}.}
#' \item{\code{"Search1",...,"Search5"}}{fate of carcass on the 1st, 2nd, 3rd,
#' 4th, and 5th search after placement. A value of 1 implies that a carcass
#' was discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{cpID}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing
#' the time the carcass was scavenged or otherwise removed from the field.
#' For example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the
#' carcass was last observed 2.04 days after being placed in the field and
#' was noted missing 3.21 days after being placed. If the precise time of
#' carcass removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date an arc at the site
#' was searched, a column of \code{SearchDate}s, and a column for each arc, and
#' one column at the end for the inner heliostat field, labeled \code{center}.
#' In addition, there is a column to indicate the \code{Season}. A column with
#' search dates and columns for each distinct area (arcs and center) searched
#' are required. Other columns are optional.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates on which an arc was searched.
#' Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone (\code{CDT})
#' is optional. A time stamp may be included if desired (e.g.,
#' \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used in place
#' of \code{-}.}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"} to indicate which season the search was conducted in.
#' \code{Season} is optional but may be used as a temporal covariate for
#' fatality estimates.}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each arc and columns for each
#' carcass size class (labels must match those of the class factors in the
#' carcass observation file). Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area). In this example, within the inner field (center)
#' observers are unobstructed in ability to discover carcasses, for a DWP of 1.
#' In the outer heliostat field observers walk along transects separated by 50
#' meters, but the entire area is surveyed, so DWP = 1.
#' \describe{
#' \item{\code{Unit}}{unique ID for each arc, plus one labeled \code{center}
#' for the inner heliostat field. IDs match those used in the \code{$CO} data
#' frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{DWP associated with size class Bat}
#' \item{\code{sml}}{DWP associated with size class Small}
#' \item{\code{med}}{DWP associated with size class Medium}
#' \item{\code{lrg}}{DWP associated with size class Large}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given
#' carcass (date found, size, species, etc.)
#' \describe{
#' \item{\code{carcID}}{unique identifier for each carcass.}
#' \item{\code{Unit}}{identifier for which unit the given carcass was found
#' at: \code{"arc19"}, \code{"arc65"}, etc, for arcs in the outer heliostat
#' field, or \code{"center"}, indicating the inner heliostat field.}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Flux}}{An optional field indicating whether there Was evidence
#' the animal was killed by flux. \code{"TRUE"}, or \code{"False"}.}
#' \item{\code{Field}}{Optional indicator of whether the animal found in the
#' \code{"inner"} or \code{"outer"} heliostat field?}
#' \item{\code{Ring}}{Optional note animals found in the outer heliostat field
#' indicating which concentric ring the carcass was found in.}
#' \item{\code{Distance}}{Optional note animals found in the outer heliostat
#' field representing the perpendicular distance from the searcher the carcass
#' was discovered at.}
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included
#' in the search schedule (\code{$SS$SearchDate}}
#' \item{\code{X}}{Distance in meters from the Western edge of the facility.}
#' \item{\code{Y}}{Distance in meters from the Southern edge of the facility.}
#' }
#'
#' @source \code{solar_powerTower}
"solar_powerTower"
ddalthorp/GenEst documentation built on June 4, 2023, 1 a.m.
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# Mock ------------------------------
#' A mock example data set
#'
#' A template dataset used for testing purposes. Dataset containing SE, CP, SS,
#' DWP, and CO data. Data are mostly random without patterns.
#'
#' @format A list with 5 items:
#' \describe{
#' \item{SE}{Searcher efficiency trial data}
#' \item{CP}{Carcass persistence trial data}
#' \item{SS}{Search schedule data}
#' \item{DWP}{Density weighted proportion of area searched data}
#' \item{CO}{Carcass observations}
#' }
#' @source \code{mock}
"mock"
# Cleared ------------------------------
#' Wind cleared plot (60m) Search Example
#'
#' A complete example data set for estimating fatalities from 60 m cleared plots
#' at 23 out of 100 searches at a wind power facility. Data on carcass
#' observations (CO) from a search of all terrain out to 60m from each of 100
#' turbines at a theoretical site, field trials for estimating carcass
#' persistence (CP) and searcher efficiency (SE), search schedule (SS)
#' parameters (for example, which turbines were searched on which days), and
#' density weighted proportion (DWP) of area searched at each turbine (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{wind_cleared} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#'
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{pkID}}{unique ID for each carcass}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{Visibility}}{indicator for visibility class of the ground, with
#' \code{"RP"} for carcasses placed on a road or turbine pad, \code{"M"}
#' for moderate visibility (e.g., plowed field; short, sparse vegetation),
#' or \code{"D"} for difficult visibility}
#' \item{\code{"s1",...,"s5"}}{fate of carcass on the 1st, 2nd, 3rd, 4th, and
#' 5th search after placement. A value of 1 implies that a carcass was
#' discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "SN" could be used to indicate that the
#' turbine was not searched because of snow, or "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' }
#'
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{cpID}}{unique ID for each carcass}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{Visibility}}{indicator for visibility class of the ground, with
#' \code{"RP"} for carcasses placed on a road or turbine pad, \code{"M"} for
#' moderate visibility (e.g., plowed field; short, sparse vegetation), or
#' \code{"D"} for difficult visibility.} \item{\code{LastPresent},
#' \code{FirstAbsent}}{endpoints of the interval bracketing the time the carcass
#' was scavenged or otherwise removed from the field. For example,
#' \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the carcass was
#' last observed 2.04 days after being placed in the field and was noted
#' missing 3.21 days after being placed. If the precise time of carcass
#' removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date a turbine at the site
#' was searched, a column of \code{SearchDate}s, and a column for each turbine.
#' In addition, there is a column to indicate the \code{Season}. A column with
#' search dates and columns for each turbine searched are required. Other
#' columns are optional.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates on which at least one turbine was
#' searched. Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone
#' (\code{CDT}) is optional. A time stamp may be included if desired (e.g.,
#' \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used in place
#' of \code{-}.}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"} to
#' indicate which season the search was conducted in. \code{Season} is
#' optional but may be used as a temporal covariate for fatality estimates.}
#' \item{\code{t1}, etc.}{unique ID for all turbines that were searched on at
#' least one search date. Values are either 1 or 0, indicating whether the
#' given turbine (column) was searched or not on the given date (row).}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each turbine and columns for
#' each carcass size class. Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area).
#' \describe{
#' \item{\code{Turbine}}{unique ID for each turbine. IDs match those used in
#' the \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{Size}}{\code{bat}, \code{sml}, \code{med}, \code{lrg}}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"} to
#' indicate which season the search was conducted in. \code{Season} is
#' optional but may be used as a temporal covariate for fatality estimates.}}
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given carcass
#' (date found, size, species, etc.)
#' \describe{
#' \item{\code{carcID}}{unique identifier for each carcass: \code{"x30"},
#' \code{"x46"}, etc.}
#' \item{\code{Turbine}}{identifier for which turbine the given carcass was
#' found at: \code{"t19"}, \code{"t65"}, \code{"t49"}, etc.}
#' \item{\code{TurbineType}}{the type of turbine: \code{"X"}, \code{"Y"} or
#' \code{"Z"}. }
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included
#' in the search schedule (\code{$SS$SearchDate})}
#' \item{\code{Visibility}}{visibility class: \code{"RP"}, \code{"M"}, or
#' \code{"D"}, as described in \code{$CP} and \code{$SE}}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{SpeciesGroup}}{species group: \code{"bat0"}, \code{"bat1"},
#' \code{"brd1"}, \code{"brd2"}, \code{"brd3"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Distance}}{distance from the turbine}
#' }
#'
#' @source \code{wind_cleared}
"wind_cleared"
# RP ------------------------------
#' Wind Road and Pad (120m) Example
#'
#' This example dataset is based on 120 m radius road and pad searches of all
#' 100 turbines at a theoretical site. The simulated site consists of 100
#' turbines, searched on roads and pads only, out to 120 meters. Search
#' schedule differs by turbine and season, with more frequent searches in the
#' fall, and a subset of twenty turbines searched at every scheduled search.
#'
#' Data on carcass observations (CO) from searches, field trials for estimating
#' carcass persistence (CP) and searcher efficiency (SE), search schedule (SS)
#' parameters (for example, which turbines were searched on which days), and
#' density weighted proportion (DWP) of area searched at each turbine (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{wind_RP} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#'
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{pkID}}{unique ID for each carcass}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{"s1",...,"s5"}}{fate of carcass on the 1st, 2nd, 3rd, 4th, and
#' 5th search after placement. A value of 1 implies that a carcass was
#' discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "SN" could be used to indicate that the
#' turbine was not searched because of snow, or "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{cpID}}{unique ID for each carcass}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird.}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing the
#' time the carcass was scavenged or otherwise removed from the field. For
#' example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the carcass
#' was last observed 2.04 days after being placed in the field and was noted
#' missing 3.21 days after being placed. If the precise time of carcass
#' removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date a turbine at the site
#' was searched, a column of \code{SearchDate}s, and a column for each turbine.
#' In addition, there is a column to indicate the \code{Season}. A column with
#' search dates and columns for each turbine searched are required. Other
#' columns are optional.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates on which at least one turbine was
#' searched. Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone
#' (\code{CDT}) is optional. A time stamp may be included if desired
#' (e.g., \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used
#' in place of \code{-}.}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"} to
#' indicate which season the search was conducted in. \code{Season} is
#' optional but may be used as a temporal covariate for fatality estimates.}
#' \item{\code{t1}, etc.}{unique ID for all turbines that were searched on at
#' least one search date. Values are either 1 or 0, indicating whether the
#' given turbine (column) was searched or not on the given date (row).}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each turbine and columns for
#' each carcass size class. Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area).
#' \describe{
#' \item{\code{Turbine}}{unique ID for each turbine. IDs match those used in
#' the \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{DWP associated with size class Bat.}
#' \item{\code{sml}}{DWP associated with size class Small.}
#' \item{\code{med}}{DWP associated with size class Medium.}
#' \item{\code{lrg}}{DWP associated with size class Large.}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given
#' carcass (date found, size, species, etc.)
#' \describe{
#' \item{\code{carcID}}{unique identifier for each carcass: \code{"x30"},
#' \code{"x46"}, etc.}
#' \item{\code{Turbine}}{identifier for which turbine the given carcass was
#' found at: \code{"t19"}, \code{"t65"}, \code{"t49"}, etc.}
#' \item{\code{TurbineType}}{the type of turbine: \code{"X"}, \code{"Y"} or
#' \code{"Z"}. }
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included
#' in the search schedule (\code{$SS$SearchDate}}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{SpeciesGroup}}{species group: \code{"bat0"}, \code{"bat1"},
#' \code{"brd1"}, \code{"brd2"}, \code{"brd3"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Distance}}{distance from the turbine}
#' }
#'
#' @source \code{wind_RP}
"wind_RP"
# RPbat ------------------------------
#' Wind Bat-Only Road and Pad (120m) Example
#'
#' This example dataset considers only bats found on 120 m radius road and pad
#' searches of all 100 turbines at a theoretical site. The simulated site
#' consists of 100 turbines, searched on roads and pads only, out to 120
#' meters. Search schedule differs by turbine and season, with more frequent
#' searches in the fall, and a subset of twenty turbines searched at every
#' scheduled search.
#'
#' Data on carcass observations (CO) from searches, field trials for estimating
#' carcass persistence (CP) and searcher efficiency (SE), search schedule (SS)
#' parameters (for example, which turbines were searched on which days), and
#' density weighted proportion (DWP) of area searched at each turbine (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{wind_RPbat} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#'
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{pkID}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{"s1",...,"s5"}}{fate of carcass on the 1st, 2nd, 3rd, 4th, and
#' 5th search after placement. A value of 1 implies that a carcass was
#' discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "SN" could be used to indicate that the
#' turbine was not searched because of snow, or "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{cpID}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"}}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing
#' the time the carcass was scavenged or otherwise removed from the field.
#' For example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the
#' carcass was last observed 2.04 days after being placed in the field and
#' was noted missing 3.21 days after being placed. If the precise time of
#' carcass removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date a turbine at the site
#' was searched, a column of \code{SearchDate}s, and a column for each turbine.
#' In addition, there is a column to indicate the \code{Season}. A column with
#' search dates and columns for each turbine searched are required. Other
#' columns are optional.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates on which at least one turbine was
#' searched. Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone
#' (\code{CDT}) is optional. A time stamp may be included if desired
#' (e.g., \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used
#' in place of \code{-}.}
#' \item{\code{Season}}{\code{"spring"}, \code{"summer"}, or \code{"fall"} to
#' indicate which season the search was conducted in. \code{Season} is
#' optional but may be used as a temporal covariate for fatality estimates.}
#' \item{\code{t1}, etc.}{unique ID for all turbines that were searched on at
#' least one search date. Values are either 1 or 0, indicating whether the
#' given turbine (column) was searched or not on the given date (row).}
#' }
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each turbine and columns for
#' each carcass size class. Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area).
#' \describe{
#' \item{\code{Turbine}}{unique ID for each turbine. IDs match those used in
#' the \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{Contains the DWP for each turbine, with respect to size
#' class (in this case, bats only.}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given
#' carcass (date found, size, species, etc.)
#' \describe{
#' \item{\code{carcID}}{unique identifier for each carcass: \code{"x30"},
#' \code{"x46"}, etc.}
#' \item{\code{Turbine}}{identifier for which turbine the given carcass was
#' found at: \code{"t19"}, \code{"t65"}, \code{"t49"}, etc.}
#' \item{\code{TurbineType}}{the type of turbine: \code{"X"}, \code{"Y"} or
#' \code{"Z"}. }
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included
#' in the search schedule (\code{$SS$SearchDate}}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{SpeciesGroup}}{species group: \code{"bat0"}, \code{"bat1"},
#' \code{"brd1"}, \code{"brd2"}, \code{"brd3"}}
#' \item{\code{Distance}}{Distance from the turbine.}
#' }
#' @source \code{wind_RPbat}
"wind_RPbat"
# Trough ------------------------------
#' Trough-based solar thermal power simulated example
#'
#' An example data set for estimating fatalities from a trough-based solar
#' thermal electric power generation facility. The simulated site is inspected
#' daily along ten 2000 meter long transects, which run north-south. Observers
#' look up to 150 meters away down the rows created by troughs (east-west).
#' One sided distance sampling will be used, with observers looking consistently
#' in one cardinal direction as they travel through the facility. A sitewide
#' clearout search is implemented before the first scheduled winter search.
#'
#' The dataset consists of five parts: Data on carcass observations (CO) from
#' daily searches, field trials for estimating carcass persistence (CP) and
#' searcher efficiency (SE), search schedule (SS), and density weighted
#' proportion (DWP) of area searched for the rows within each transect (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{solar_trough} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{"Search1",...,"Search5"}}{fate of carcass on the 1st, 2nd, 3rd,
#' 4th, and 5th search after placement. A value of 1 implies that a carcass
#' was discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' \item{\code{Distance}}{the distance a carcass was placed from the
#' observer's transect.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{Index}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing the
#' time the carcass was scavenged or otherwise removed from the field. For
#' example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the carcass
#' was last observed 2.04 days after being placed in the field and was noted
#' missing 3.21 days after being placed. If the precise time of carcass
#' removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it was
#' observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date a transect at the site
#' was searched, a column of \code{SearchDate}s, and a column for each
#' transect. In addition, there is an optional column to indicate the
#' \code{Season}. The columns for distinct area (array) and the date column
#' are required, and the names of the columns for search areas must match the
#' names of areas used in the DWP and CO files.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates when a transect was searched.
#' Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone (\code{CDT})
#' is optional. A time stamp may be included if desired (e.g.,
#' \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used in
#' place of \code{-}.}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"} to indicate which season the search was conducted in.
#' \code{Season} is optional but may be used as a temporal covariate for
#' fatality estimates.}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each transect and columns for
#' each carcass size class (labels must match those of the class factors in the
#' carcass observation file). Values represent the density-weighted proportion
#' of the searched area for each size (or the fractionof carcasses that fall
#' in the searched area). Since the whole site was searched, DWP is uniformly
#' set equal to 1.
#' \describe{
#' \item{\code{Unit}}{unique ID for each transect. IDs match those used in
#' the \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{DWP associated with size class Bat}
#' \item{\code{sml}}{DWP associated with size class Small}
#' \item{\code{med}}{DWP associated with size class Medium}
#' \item{\code{lrg}}{DWP associated with size class Large}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given carcass
#' (date found, size, species, etc.)
#' \describe{
#' \item{\code{Index}}{unique identifier for each carcass.}
#' \item{\code{Unit}}{identifier for which transect the given carcass was
#' found at. Values must match with DWP Transect values Search Schedule
#' column names.}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Row}}{Optional indicator of which row within an array a carcass
#' was found at.}
#' \item{\code{Distance}}{The perpendicular distance from the searcher's
#' transect at which the carcass was discovered at.}
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}.
#' Every date entered here is (and must be) included in the search schedule
#' (\code{$SS$SearchDate})}
#' \item{\code{X}}{UTM Easting of carcass.}
#' \item{\code{Y}}{UTM Northing of carcass.}
#' }
#'
#' @source \code{solar_trough}
"solar_trough"
# PV ------------------------------
#' Photovoltaic Example Dataset
#'
#' An example data set for estimating fatalities from a large photovoltaic solar
#' generation facility.
#'
#' The simulated site is organized into 300 arrays of panels. As observers walk
#' north-south along paths between arrays, they look east or west down rows
#' between solar panels 150 meters long, with 38 searchable rows per array.
#' Observers consistently look for animals down one cardinal direction, making
#' this a one-sided distance sample. Searches are scheduled on a seven day
#' rotation, with 60 arrays searched per weekday. A sitewide clearout search
#' is implemented before the first scheduled winter search.
#'
#' The dataset consists of five parts: Data on carcass observations (CO) from
#' array searches, field trials for estimating carcass persistence (CP) and
#' searcher efficiency (SE), search schedule (SS), and density weighted
#' proportion (DWP) of area searched at each array (which is an area adjustment
#' factor to account for incomplete search coverage).
#'
#' @format \code{solar_PV} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{"Search1",...,"Search5"}}{fate of carcass on the 1st, 2nd, 3rd,
#' 4th, and 5th search after placement. A value of 1 implies that a carcass
#' was discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' \item{\code{Distance}}{the distance a carcass was placed from the
#' observer's transect. Used in determining probability to detect with
#' distance sampling.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{Index}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing
#' the time the carcass was scavenged or otherwise removed from the field.
#' For example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the
#' carcass was last observed 2.04 days after being placed in the field and
#' was noted missing 3.21 days after being placed. If the precise time of
#' carcass removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date an array at the site was
#' searched, a column of \code{SearchDate}s, and a column for each array. In
#' addition, there is an optional column to indicate the \code{Season}. The
#' columns for distinct area (array) and the date column are required, and the
#' names of the columns for search areas must match the names of areas used in
#' the DWP and CO files.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates when arrays were searched. Format
#' in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone (\code{CDT}) is
#' optional. A time stamp may be included if desired (e.g.,
#' \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used in
#' place of \code{-}.}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"},
#' or \code{"fall"} to indicate which season the search was conducted in.
#' \code{Season} is optional but may be used as a temporal covariate for
#' fatality estimates.}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each array and columns for each
#' carcass size class (labels must match those of the class factors in the
#' carcass observation file). Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area). In this example, observers walk along transects
#' separated by 150 meters, and search coverage is assumed to be 100%, i.e.,
#' DWP = 1 for each unit. This requires that carcasses be placed at random
#' locations in the field, even at distances from the transects that would make
#' it unlikely to observe small carcasses.
#' \describe{
#' \item{\code{Unit}}{unique ID for each array. IDs match those used in the
#' \code{$CO} data frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{DWP associated with size class Bat}
#' \item{\code{sml}}{DWP associated with size class Small}
#' \item{\code{med}}{DWP associated with size class Medium}
#' \item{\code{lrg}}{DWP associated with size class Large}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given
#' carcass (date found, size, species, etc.)
#' \describe{
#' \item{\code{Index}}{unique identifier for each carcass.}
#' \item{\code{Unit}}{identifier for which unit the given carcass was found
#' at: \code{"arc19"}, \code{"arc65"}, etc, for arcs in the outer heliostat
#' field, or \code{"center"}, indicating the inner heliostat field.}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Row}}{Optional indicator of which row within an array a carcass
#' was found at.}
#' \item{\code{Distance}}{The perpendicular distance from the searcher's
#' transect at which the carcass was discovered at.}
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included in
#' the search schedule
#' (\code{$SS$SearchDate}}
#' \item{\code{X}}{UTM Easting of carcass.}
#' \item{\code{Y}}{UTM Northing of carcass.}
#' }
#'
#' @source \code{solar_PV}
"solar_PV"
# Power Tower ------------------------------
#' Power Tower Example Dataset
#'
#' An example data set for estimating fatalities from a concentrating
#' solar-thermal (power tower) generation facility.
#'
#' The simulated site consists of a single tower generating approximately 130
#' MW. The tower is surrounded by a 250 meter radius circular inner field of
#' heliostats, searched on a weekly schedule. From the inner circle, 18
#' concentric rings of heliostats 50 meters deep extend to the boundaries of the
#' simulated site. Rings are subdivided into 8 arcs each, with arcs 1-8
#' immediately adjacent to the central circle. Arcs are search using distance
#' sampling techniques on a weekly schedule, with 29 arcs searched per weekday.
#'
#' There are two sources of mortality simulated: flux and non-flux (collision or
#' unknown cause).Flux carcasses are generated (weibull) about the tower, with
#' 5\% to be found in the outer field. Non-flux mortality is assumed uniform
#' across the site.
#'
#' The dataset consists of five parts: Data on carcass observations (CO) from
#' inner and outer heliostat searches, field trials for estimating carcass
#' persistence (CP) and searcher efficiency (SE), search schedule (SS), and
#' density weighted proportion (DWP) of area searched at each turbine (which is
#' an area adjustment factor to account for incomplete search coverage).
#'
#' @format \code{solar_powerTower} is a list with 5 elements:
#' \describe{
#' \item{\code{SE}}{Searcher efficiency trial data}
#' \item{\code{CP}}{Carcass persistence trial data}
#' \item{\code{SS}}{Search schedule parameters}
#' \item{\code{DWP}}{Density weighted proportion of area searched}
#' \item{\code{CO}}{Carcass observations}
#' }
#' @section Searcher Efficiency (\code{SE}):
#' \code{$SE} is a data frame with each row representing the fate of a single
#' carcass in the searcher efficiency trials. There are columns for:
#' \describe{
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{Field}}{indicates carcass placed in inner or outer heliostat
#' field, with levels \code{"inner"} or \code{outer}.}
#' \item{\code{"Search1",...,"Search5"}}{fate of carcass on the 1st, 2nd, 3rd,
#' 4th, and 5th search after placement. A value of 1 implies that a carcass
#' was discovered by searchers, 0 implies the carcass was present but not
#' discovered, and any other value is interpreted as "no search" or
#' "carcass not present" and ignored in the model. In this data set,
#' \code{NA} indicates that a carcass had been previously discovered and
#' removed from the field. A user may use a variety of values to
#' differentiate different reasons no search was conducted or the carcass
#' was not present. For example, "NS" to indicate the search
#' was not scheduled in that location at that time, or "SC" to indicate the
#' carcass had been removed by scavengers prior to the search.}
#' }
#' @section Carcass Persistence (\code{CP}):
#' \code{$CP} is a data frame with each row representing the fate of a single
#' carcass in the carcass persistence trials. There are columns for:
#' \describe{
#' \item{\code{cpID}}{unique ID for each carcass}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Size}}{\code{"bat"}; or \code{"lrg"}, \code{"med"}, or
#' \code{"sml"} bird}
#' \item{\code{LastPresent}, \code{FirstAbsent}}{endpoints of the interval bracketing
#' the time the carcass was scavenged or otherwise removed from the field.
#' For example, \code{LastPresent = 2.04}, \code{FirstAbsent = 3.21} indicates that the
#' carcass was last observed 2.04 days after being placed in the field and
#' was noted missing 3.21 days after being placed. If the precise time of
#' carcass removal is known (e.g., recorded by camera), then \code{LastPresent} and
#' \code{FirstAbsent} should be set equal to each other. If a carcass persists
#' beyond the last day of the field trial, \code{LastPresent} is the last time it
#' was observed and \code{FirstAbsent} is entered as \code{Inf} or \code{NA}.}
#' }
#'
#' @section Search Schedule (\code{SS}):
#' \code{$SS} is a data frame with a row for each date an arc at the site
#' was searched, a column of \code{SearchDate}s, and a column for each arc, and
#' one column at the end for the inner heliostat field, labeled \code{center}.
#' In addition, there is a column to indicate the \code{Season}. A column with
#' search dates and columns for each distinct area (arcs and center) searched
#' are required. Other columns are optional.
#' \describe{
#' \item{\code{SearchDate}}{columns of dates on which an arc was searched.
#' Format in this data is \code{"\%Y-\%m-\%d CDT"}, but time zone (\code{CDT})
#' is optional. A time stamp may be included if desired (e.g.,
#' \code{2018-03-20 02:15:41}). Alternatively, \code{\\} can be used in place
#' of \code{-}.}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"} to indicate which season the search was conducted in.
#' \code{Season} is optional but may be used as a temporal covariate for
#' fatality estimates.}
#' }
#'
#' @section Density Weighted Proportion (\code{DWP}):
#' \code{$DWP} is a data frame with a row for each arc and columns for each
#' carcass size class (labels must match those of the class factors in the
#' carcass observation file). Values represent the density-weighted proportion
#' of the searched area for each size (or the fraction of carcasses that fall
#' in the searched area). In this example, within the inner field (center)
#' observers are unobstructed in ability to discover carcasses, for a DWP of 1.
#' In the outer heliostat field observers walk along transects separated by 50
#' meters, but the entire area is surveyed, so DWP = 1.
#' \describe{
#' \item{\code{Unit}}{unique ID for each arc, plus one labeled \code{center}
#' for the inner heliostat field. IDs match those used in the \code{$CO} data
#' frame and the column names in the \code{$SS} data.}
#' \item{\code{bat}}{DWP associated with size class Bat}
#' \item{\code{sml}}{DWP associated with size class Small}
#' \item{\code{med}}{DWP associated with size class Medium}
#' \item{\code{lrg}}{DWP associated with size class Large}
#' }
#'
#' @section Carcass Observations (\code{CO}):
#' \code{$CO} is a data frame with a row for carcass observed in the carcass
#' searches and a number of columns giving information about the given
#' carcass (date found, size, species, etc.)
#' \describe{
#' \item{\code{carcID}}{unique identifier for each carcass.}
#' \item{\code{Unit}}{identifier for which unit the given carcass was found
#' at: \code{"arc19"}, \code{"arc65"}, etc, for arcs in the outer heliostat
#' field, or \code{"center"}, indicating the inner heliostat field.}
#' \item{\code{Species}}{species of the carcass: \code{"BA"}, \code{"BB"},
#' \code{"BC"}, \code{"BD"}, \code{"BE"}, \code{"LA"}, \code{"LB"},
#' \code{"LD"}, \code{"LE"}, \code{"MA"}, \code{"MB"}, \code{"SA"},
#' \code{"SB"}, \code{"SC"}, \code{"SD"}, \code{"SE"}, \code{"SF"},
#' \code{"SG"}}
#' \item{\code{Size}}{size: \code{"bat"}, \code{"lrg"}, \code{"med"},
#' \code{"sml"}}
#' \item{\code{Season}}{\code{"winter"}, \code{"spring"}, \code{"summer"}, or
#' \code{"fall"}}
#' \item{\code{Flux}}{An optional field indicating whether there Was evidence
#' the animal was killed by flux. \code{"TRUE"}, or \code{"False"}.}
#' \item{\code{Field}}{Optional indicator of whether the animal found in the
#' \code{"inner"} or \code{"outer"} heliostat field?}
#' \item{\code{Ring}}{Optional note animals found in the outer heliostat field
#' indicating which concentric ring the carcass was found in.}
#' \item{\code{Distance}}{Optional note animals found in the outer heliostat
#' field representing the perpendicular distance from the searcher the carcass
#' was discovered at.}
#' \item{\code{DateFound}}{dates entered in the same format as in
#' \code{$SS$SearchDate}. Every date entered here is (and must be) included
#' in the search schedule (\code{$SS$SearchDate}}
#' \item{\code{X}}{Distance in meters from the Western edge of the facility.}
#' \item{\code{Y}}{Distance in meters from the Southern edge of the facility.}
#' }
#'
#' @source \code{solar_powerTower}
"solar_powerTower"
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