weightAssign: Calculate Weights for Isotope Assignments weightAssign

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

Calculate Weights for Isotope Assignments weightAssign

Description

The primary purpose of this function is to determine whether weighting likelihood based isotope assignments and prior information, such as relative abundance can improve the model performance compared to the isotope-only model. To do this, we raise the likelihood and prior values to powers from 0.1 to 10 and measure model performance using the assignment error rate and assignment area. Weights < 1 flatten the likelihood/prior distributions (giving relatively more weight to smaller values) and weights > 1 sharpen the distributions (giving relatively less weight to smaller values. The weightAssign function generates origin assignments using stable-hydrogen isotopes in tissue. If first generates a probability surface of origin assignment from a vector of stable-isotope values for each animal/sample captured at a known location. Probabilistic assignments are constructed by first converting observed stable-isotope ratios (isoscape) in either precipitation or surface waters into a 'tissuescape' using a user-provided intercept, slope and standard deviation. See Hobson et. al. (2012).

Usage

weightAssign(
  knownLocs,
  isovalues,
  isoSTD,
  intercept,
  slope,
  odds = 0.67,
  relAbund,
  weightRange = c(-1, 1),
  sppShapefile = NULL,
  assignExtent = c(-179, -60, 15, 89),
  element = "Hydrogen",
  surface = FALSE,
  period = "Annual",
  verbose = 1,
  mapDirectory = NULL
)

Arguments

knownLocs	matrix of capture locations of the same length as isovalues
isovalues	vector of tissue isotope values from known locations
isoSTD	standard deviation from calibration
intercept	intercept value from calibration
slope	value from calibration
odds	odds ratio to use to set likely and unlikely locations defaults to 0.67
relAbund	raster layer of relative abundance that sums to 1.
weightRange	vector of length 2 within minimum and maximum values to weight isotope and relative abundance. Default = c(-1,1)
sppShapefile	A polygon spatial layer (sf - MULTIPOLYGON) defining species range. Assignments are restricted to these areas.
assignExtent	definition for the extent of the assignment. Can be used in place of sppShapefile to limit assignment. Input should follow c(xmin,xmax,ymin,ymax) in degrees longitude and latitude.
element	The elemental isotope of interest. Currently the only elements that are implemented are 'Hydrogen' (default) and 'Oxygen'
surface	DEPRECATED function no longer returns surface water values. Default is 'FALSE' which returns the precipitation isotopes ratio.
period	The time period of interest. If 'Annual' returns a raster of mean annual values in precipitation for the element. If 'GrowingSeason' returns growing season values in precipitation for element of interest.
verbose	takes values 0 or 1 (default). 0 prints no output during run. 1 prints a message detailing where in the process the function is.
mapDirectory	Directory to save/read isotope map from. Can use relative or absolute addressing. The default value (NULL) downloads to a temporary directory, so we strongly recommend changing this from the default unless you're sure you're not going to need these data more than once.

Value

returns an weightAssign object containing the following:

top

data.frame with the optimal weightings

frontier

data.frame with values that fall along the Pareto frontier

performance

data.frame with error rate and assignment area for each weight combination

References

Cohen, E. B., C. S. Rushing, F. R. Moore, M. T. Hallworth, J. A. Hostetler, M. Gutierrez Ramirez, and P. P. Marra. 2019. The strength of migratory connectivity for birds en route to breeding through the Gulf of Mexico. Ecography 42: 658-669.

Rushing, C. S., P. P. Marra and C. E. Studds. 2017. Incorporating breeding abundance into spatial assignments on continuous surfaces. Ecology and Evolution 3: 3847-3855. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/ece3.2605")}

Cohen, E. B., C. S. Rushing, F. R. Moore, M. T. Hallworth, J. A. Hostetler, M. Gutierrez Ramirez, and P. P. Marra. 2019. The strength of migratory connectivity for birds en route to breeding through the Gulf of Mexico. Ecography 42: 658-669.

Hobson, K. A., S. L. Van Wilgenburg, L. I. Wassenaar, and K. Larson. 2012. Linking hydrogen isotopes in feathers and precipitation: sources of variance and consequences for assignment to isoscapes. PLoS ONE 7: e35137.

Rushing, C. S., P. P. Marra, and C. E. Studds. 2017. Incorporating breeding abundance into spatial assignments on continuous surfaces. Ecology and Evolution 7: 3847-3855.

Examples

extensions <- c("shp", "shx", "dbf", "sbn", "sbx")
tmp <- tempdir()
for (ext in extensions) {
download.file(paste0(
              "https://raw.githubusercontent.com/SMBC-NZP/MigConnectivity",
                     "/master/data-raw/Spatial_Layers/OVENdist.",
                     ext),
              destfile = paste0(tmp, "/OVENdist.", ext), mode = "wb")
}
OVENdist <- sf::st_read(paste0(tmp, "/OVENdist.shp"))
OVENdist <- OVENdist[OVENdist$ORIGIN==2,] # only breeding
sf::st_crs(OVENdist) <- sf::st_crs(4326)

download.file(paste0("https://raw.githubusercontent.com/SMBC-NZP/MigConnectivity",
                     "/master/data-raw/deltaDvalues.csv"),
              destfile = paste0(tmp, "/deltaDvalues.csv"))
OVENvals <- read.csv(paste0(tmp, "/deltaDvalues.csv"))

HBEFbirds <- OVENvals[grep("NH",OVENvals[,1]),]

# Create a spatial object of known capture sites
knownLocs <- sf::st_as_sf(data.frame(Long = rep(-73,nrow(HBEFbirds)),
                                    Lat = rep(43,nrow(HBEFbirds))),
                         coords = c("Long","Lat"),
                         crs = 4326)

#Get OVEN abundance from BBS estimates and read into R #
utils::download.file("https://www.mbr-pwrc.usgs.gov/bbs/ra15/ra06740.zip",
                     destfile = paste0(tmp, "/oven.zip"))
utils::unzip(paste0(tmp, "/oven.zip"), exdir = tmp)
oven_dist <- sf::st_read(paste0(tmp, "/ra06740.shp"))

# Empty raster with the same dimensions as isoscape and Ovenbird distribution

# We do this manually here but the weightedAssign function has been updated
# to ensure the isoscape and abundance rasts have the same extent using
# resampling to match  relAbund to the isoscape.
r <- terra::rast(nrow = 331, ncol = 870,
                 res = c(0.0833333, 0.0833333),
                 xmin = -125.1667, xmax = -52.66672,
                 ymin = 33.49995, ymax = 61.08327,
                 crs = sf::st_crs(4326)$wkt)

# rasterize the polygons from BBS - this is not needed if working with a
# rasterized surface
relativeAbun<-terra::rasterize(terra::vect(sf::st_transform(oven_dist,4326)),
                               r,
                               field = "RASTAT")

relativeAbund <- relativeAbun/terra::global(relativeAbun, sum,
                                            na.rm = TRUE)$sum


BE <- weightAssign(knownLocs = knownLocs,
                   isovalues = HBEFbirds[,2],
                   isoSTD = 12,
                   intercept = -10,
                   slope = 0.8,
                   odds = 0.67,
                   relAbund = relativeAbund,
                   weightRange = c(-1, 1),
                   sppShapefile = OVENdist,
                   assignExtent = c(-179,-60,15,89),
                   element = "Hydrogen",
                   period = "Annual")

SMBC-NZP/MigConnectivity documentation built on March 26, 2024, 4:22 p.m.