R/data.R

In SMBC-NZP/MigConnectivity: Estimate Migratory Connectivity for Migratory Animals

#' Example transition probabilities (psis) between origin and target sites
#'
#' A dataset containing example psi matrices used in Cohen et al. (2018).
#'
#' @format A named list with 8 transition probability matrices in it. The
#' direction is from origin site (rows) to target sites (columns), so each
#' row of each matrix sums to 1.  The psi matrices are:
#' \itemize{
#'   \item Full Mix: Full mixing from all origin sites to all target sites
#'   \item Avoid One Site: All origin sites have the same transition
#'      probabilities, mostly avoiding target site 4
#'   \item Full Connectivity: Each origin site transitions to only one target
#'      site
#'   \item Half Mix: Origin sites A and B mix fully between target sites 1 and
#'      2, but don't move to target sites 3 or 4, while origin sites C and D
#'      mix fully between target sites 3 and 4, but don't move to target sites
#'      1 or 2
#'   \item Low: Simulation scenario labelled "Moderate Connectivity" in Cohen
#'      et al. (2014)
#'   \item Medium: Simulation scenario labelled "Strong Connectivity" in Cohen
#'      et al. (2014)
#'   \item One Site Preference: Three origin sites have full mixing, but origin
#'      site D only goes to target site 4
#'   \item Negative: Artificial transition probability scenario developed to
#'      produce a negative MC value under some circumstances
#' }
"samplePsis"

#' Example origin and target site positions and distances on a 2-D plane
#'
#' \code{sampleOriginPos} is a dataset containing example origin site positions
#' from 12 scenarios used in Cohen et al. (2018).  For the same 12
#' scenarios, \code{sampleOriginDist} contains the origin site distances,
#' \code{sampleTargetPos} contains the target site positions, and
#' \code{sampleTargetDist} contains the target site distances.
#'
#' @format Each dataset is a named list with 12 matrices in it, representing 12
#' scenarios. The position matrices each have 2 columns (x and y position) and
#' 4 rows (for each origin or target site).  The distance matrices are
#' symmetrical and 4 x 4. The 12 scenarios are:
#' \itemize{
#'   \item Linear: Both origin and target sites arranged in horizontal linear
#'      fashion, with equal distances between each adjacent site
#'   \item B Dist BC*2: Linear, but the central origin sites are twice as far
#'      from each other as the edge sites are from the adjacent origin sites
#'   \item B Dist BC/2: Linear, but the central origin sites are half as far
#'      from each other as the edge sites are from the adjacent origin sites
#'   \item B Dist CD*2: Linear, but the last two origin sites are twice as far
#'      from each other as the other adjacent origin sites
#'   \item B Dist CD/2: Linear, but the last two origin sites are half as far
#'      from each other as the other adjacent origin sites
#'   \item B Grid: Origin sites arranged on a grid, target sites arranged
#'      linearly, both with all adjacent sites (excluding diagonals)
#'      equidistant
#'   \item NB Dist 23*2: Linear, but the central target sites are twice as far
#'      from each other as the edge sites are from the adjacent target sites
#'   \item NB Dist 23/2: Linear, but the central target sites are half as far
#'      from each other as the edge sites are from the adjacent target sites
#'   \item NB Dist 34*2: Linear, but the last two target sites are twice as far
#'      from each other as the other adjacent target sites
#'   \item NB Dist 34/2: Linear, but the last two target sites are half as far
#'      from each other as the other adjacent target sites
#'   \item NB Grid: Target sites arranged on a grid, origin sites arranged
#'      linearly, both with all adjacent sites (excluding diagonals)
#'      equidistant
#'   \item B/NB Grid: Origin and target sites each arranged on a grid, both
#'      with all adjacent sites (excluding diagonals) equidistant
#' }
"sampleOriginPos"

#' @rdname sampleOriginPos
"sampleOriginDist"

#' @rdname sampleOriginPos
"sampleTargetPos"

#' @rdname sampleOriginPos
"sampleTargetDist"

#' Example origin site abundances and relative abundances
#'
#' \code{sampleOriginN} is a dataset containing example origin site abundances
#' from 5 scenarios used in Cohen et al. (2018).  For the same 5
#' scenarios, \code{sampleOriginRelN} contains the relative abundances.
#'
#' @format Each dataset is a named list with 5 vectors in it. Each vector has
#' 4 elements (for the 4 origin sites).  The relative abundance vectors each
#' sum to 1. The 5 scenarios are:
#' \itemize{
#'   \item Base: Equal abundance at each origin site
#'   \item B Doub: The second origin site has twice the abundance of the other
#'      three sites
#'   \item B Half: The second origin site has half the abundance of the other
#'      three sites
#'   \item D Doub: The last origin site has twice the abundance of the other
#'      three sites
#'   \item D Half: The last origin site has half the abundance of the other
#'      three sites
#' }
"sampleOriginN"

#' @rdname sampleOriginN
"sampleOriginRelN"

#' Example relative abundance estimates from simulated data
#'
#' A dataset containing mcmc relative abundance estimates from simulated
#' BBS-type data from Cohen et al. (2018). Each estimate can
#' be used in \code{estStrength} function to estimate MC with uncertainty.
#'
#' @format A list with 10 mcmc (coda) estimates in it.
"abundExamples"

#' Ovenbird light-level geolocator and GPS necessary data
#'
#' Ovenbird data from Cohen et al. (2018) and Hallworth and Marra (2015).
#'
#' @format A named list with the necessary data to replicate the analyses
#' found in Cohen et al. (2018) with archival light-level geolocator and
#' GPS data.
#' The data contained in the list are:
#' \itemize{
#'   \item geo.bias: Archival light-level geolocator bias estimates.
#'        Location bias estimates in light-level geolocator estimates calculated
#'        using birds captured at known locations in Florida, Jamaica and Puerto Rico.
#'         Location bias is reported in meters and is a vector of length two with bias
#'         estimates in geolocator locations.
#'         Format: A vector of length two with bias estimates in geolocator locations.
#'   \item geo.vcov: Covariance estimates in light-level geolocator estimates calculated
#'         using birds captured at known locations in Florida, Jamaica, and Puerto Rico.
#'         Covariance is reported in meters.
#'         Format:  A 2x2 matrix of covariance estimates.
#'   \item isGL: Archival light-level geolocator or PinPoint-10 GPS tag
#'          \code{logical} vector indicating whether location estimates were obtained with a
#'          light-level geolocator (\code{TRUE}) or PinPoint-10 GPS tag (\code{FALSE}).
#'          Format:  \code{logical} of length 39
#'   \item targetPoints: Non-breeding locations for 39 Ovenbirds caught during the breeding
#'         season who carried either a light-level geolocator or PinPoint-10 GPS tag.
#'         Ovenbirds were captured at Hubbard Brook Experimental Forest, NH and Jug Bay Wetland
#'         Sanctuary, MD. These data are used as \code{originPoints} in the \code{estMC} function.
#'          \code{coords.x1} and \code{coords.x2} represent the longitude and latitude of the
#'          capture sites, respectively. The data are projected in Lambert Conformal Conic.
#'         Format:  \code{SpatialPoints}
#'         "+proj=aea +lat_1=20 +lat_2=60 +lat_0=40 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80
#'          +datum=NAD83 +units=m +no_defs +towgs84=0,0,0"
#'   \item originPoints: Capture locations for 39 Ovenbirds caught during the breeding season
#'         who carried either a light-level geolocator or PinPoint-10 GPS tag. Ovenbirds were
#'         captured at Hubbard Brook Experimental Forest, NH and Jug Bay Wetland Sanctuary, MD.
#'         These data are used as \code{originPoints} in the \code{estMC} function. \code{coords.x1}
#'         and \code{coords.x2} represent the longitude and latitude of the capture sites, respectively.
#'          The data are projected in Lambert Conformal Conic.
#'         Format:  \code{SpatialPoints}
#'   \item targetSites: Non-breeding distribution target sites used in Cohen et al. (in prep) to
#'         estimate MC of Ovenbirds tracked with light-level geolocators and PinPoint-10 GPS tags.
#'         There are three non-breeding target sites 1) Florida, United States, 2) Cuba, and 3) Hispaniola
#'         (Dominican Republic and Haiti).
#'         Format:  \code{SpatialPolygons}
#'   \item originSites: Breeding distribution origin sites used in Cohen et al. (in prep) to estimate
#'         MC of Ovenbirds tracked with light-level geolocators and PinPoint-10 GPS tags. There are two breeding
#'         origin sites, one that encompasses NH and another that encompasses MD capture deployment locations.
#'         Format: \code{SpatialPolygons}
#'   \item originRelAbund: A dataset containing relative abundance estimates from BBS data reported in Cohen et al.
#'        (in prep). These estimates can be used in \code{estMC} function as \code{originRelAbund} in conjunction
#'        with archival light-level geolocator and GPS locations.
#'        Format: A vector of length two with relative abundance estimates.
#'   \item originDist: The pairwise Great Circle Distance between the center of the polygons contained within
#'         \code{originSites}. See "Ovenbird breeding distribution origin sites" or \code{originSites}.
#'        Format: square distance matrix
#'   \item targetDist: The pairwise Great Circle Distance between the center of the polygons contained within
#'        \code{targetSites}. See "Ovenbird non-breeding distribution target sites" or \code{targetSites}.
#'        Format: square distance matrix
#' }
"OVENdata"

#' Map projections
#'
#' Map projections used when sampling from geolocator bias/error, for
#' example. The argument \code{resampleProjection} in \code{estMC} and
#' \code{estMantel} need units = m, which is true of all of these except
#' WGS84 (the second). First item is Equidistant Conic, which preserves
#' distances around latitude = 0 and longitude = 0. This is a good general
#' purpose projection, but the ideal projection may depend on the locations of
#' your points.  See names in list for suggestions. Other potential projections
#' can be found at \url{https://spatialreference.org/ref/}
#'
#' @format A named list of strings.
"projections"