---
title: '''MigConnectivity'' package: isotope simulation'
author: "Michael T. Hallworth, Jeffrey A. Hostetler"
date: '`r Sys.Date()`'
output:
rmarkdown::html_vignette: default
rmarkdown::pdf_document: default
vignette: |
%\usepackage[utf8]{inputenc}
%\VignetteIndexEntry{'MigConnectivity' package: isotope simulation}
%\VignetteEngine{knitr::rmarkdown}
---
```{r, echo = FALSE}
knitr::opts_chunk$set(collapse = TRUE,
comment = "#>",
tidy = FALSE,
message = FALSE,
warning = FALSE)
```
Load required packages
```{r eval = FALSE}
library(terra)
library(MigConnectivity)
library(sf)
```
The following is a simulation that tests the how the spatial arrangement of target sites influences MC from stable-hydrogen isotopes. The following simulation is run using data generated within the code but we use the Ovenbird as an example species.
### Ovenbird distribution
Read in the Ovenbird distribution and create a species distribution map from the abundance data.
```{r eval = FALSE}
# read in raster layer
download.file(
"https://raw.githubusercontent.com/SMBC-NZP/MigConnectivity/master/data-raw/Spatial_Layers/bbsoven.txt",
destfile = "bbsoven.txt")
OVENabund <- terra::rast("bbsoven.txt")
OVENdist <- OVENabund
OVENdist[OVENdist>0]<-1
OVENdist[OVENdist==0]<-NA
OVEN_single_poly <- terra::as.polygons(OVENdist)
terra::crs(OVEN_single_poly) <- MigConnectivity::projections$WGS84
terra::crs(OVENabund) <- MigConnectivity::projections$WGS84
```
To complete the simulation we need a template to ensure the raster resolution is the same as the assignment raster. To do this, we use the isotope data as our template. We grab the isotope base-map using the <code>getIsoMap</code> function.
```{r eval = FALSE}
### get isotope raster for template
rasterTemplate <- getIsoMap()
```
### Crop template to distribution and mask with distribution
```{r eval = FALSE}
terra::crs(rasterTemplate) <- MigConnectivity::projections$WGS84
rasterTemplate <- terra::crop(terra::mask(rasterTemplate,
OVEN_single_poly),
OVEN_single_poly)
# rasterize the distribution for relative abundance so that raster
# dimensions and resolution match the isotope layer
relativeAbund <- terra::project(OVENabund,rasterTemplate)
relativeAbund <- relativeAbund /
unlist(c(terra::global(relativeAbund, fun = "sum", na.rm = T)))
```
## Generate target sites
The simulation is focused on the effect of target sites on MC when using stable-hydrogen isotopes. The following code generates various target site layers used in the simulation.
```{r eval = FALSE}
# generate target sites
targetRanges <- vector('list',5)
# 3' latitude
targetRanges[[1]] <- terra::as.polygons(terra::rast(xmin = -180,
xmax = -40,
ymin = 25,
ymax = 85,
resolution = c(140,3)))
# 5' latitude
targetRanges[[2]] <- terra::as.polygons(terra::rast(xmin = -180,
xmax = -40,
ymin = 25,
ymax = 85,
resolution = c(140,5)))
# 10' latitude
targetRanges[[3]] <- terra::as.polygons(terra::rast(xmin = -180,
xmax = -40,
ymin = 25,
ymax = 85,
resolution = c(140,10)))
# 12 isotope units
featherIso <- (0.95*getIsoMap(period = "GrowingSeason")+(-17.57))
iso <- terra::crop(featherIso, terra::ext(c(-180,-40,25,85)))
isocut <- terra::classify(iso,
rcl = seq(terra::global(iso, fun = "min",
na.rm = TRUE)$min,
terra::global(iso, fun = "max",
na.rm = TRUE)$max,12))
targetRanges[[4]] <- terra::as.polygons(isocut)
# 12*2 isotope units
isocut <- terra::classify(iso,
rcl = seq(terra::global(iso, fun = "min",
na.rm = TRUE)$min,
terra::global(iso,fun = "max",
na.rm = TRUE)$max, 24))
targetRanges[[5]] <- terra::as.polygons(isocut)
TR <- lapply(targetRanges, sf::st_as_sf)
vTR <- lapply(TR, sf::st_make_valid)
vTR <- lapply(vTR, FUN = function(x){sf::st_set_crs(x, 4326)})
sf_use_s2(FALSE)
OVEN_single_poly <- sf::st_as_sf(OVEN_single_poly) %>% sf::st_make_valid()
# Keep only the targetSites that intersect with the OVEN polygon
targetRanges <- lapply(vTR, FUN = function(x){sf::st_intersection(x,OVEN_single_poly)})
targetRanges <- lapply(targetRanges, FUN = function(x){y <- sf::st_as_sf(x)
z <- sf::st_transform(y,4326)
return(z)})
for(i in 1:5){
targetRanges[[i]]$Target <- 1:nrow(targetRanges[[i]])
}
targetRanges <- lapply(targetRanges, sf::st_make_valid)
sf_use_s2(TRUE)
```
#### Generate simulated data
```{r, eval = FALSE}
#Generate random breeding locations using the 10' target sites
Site1 <- st_as_sf(sf::st_sample(targetRanges[[3]][1:2,], size =100, type = "random"))
Site2 <- st_as_sf(sf::st_sample(targetRanges[[3]][2:3,], size =100, type = "random"))
Site3 <- st_as_sf(sf::st_sample(targetRanges[[3]][2:4,], size =100, type = "random"))
# Capture coordinates
capCoords <- array(NA,c(3,2))
capCoords[1,] <- cbind(-98.17,28.76)
capCoords[2,] <- cbind(-93.70,29.77)
capCoords[3,] <- cbind(-85.000,29.836)
featherIso <- (0.95*getIsoMap(period = "GrowingSeason")+(-17.57))
# Extract simulated data
iso_dat <- data.frame(Site = rep(1:3, each = 100),
xcoords = c(sf::st_coordinates(Site1)[,1],
sf::st_coordinates(Site2)[,1],
sf::st_coordinates(Site3)[,1]),
ycoords = c(sf::st_coordinates(Site1)[,2],
sf::st_coordinates(Site2)[,2],
sf::st_coordinates(Site3)[,2]),
targetSite = unlist(unclass(sf::st_intersects(rbind(Site1,
Site2,
Site3),
targetRanges[[3]]))),
featherIso = terra::extract(featherIso,
terra::vect(rbind(Site1,Site2,
Site3))))
iso_dat <- iso_dat[complete.cases(iso_dat),]
# generate transition data from simulation
sim_psi <- table(iso_dat$Site, iso_dat$targetSite)
for(i in 1:nrow(sim_psi)){
sim_psi[i,]<-sim_psi[i,]/sum(sim_psi[i,])
}
states <- rnaturalearth::ne_states(country = "United States of America",
returnclass = "sf")
originSites <- states[(states$woe_name %in% c("Texas","Louisiana","Florida")),]
originSites <- sf::st_transform(originSites, 4326)
originDist <- distFromPos(st_coordinates(sf::st_centroid(originSites,
byid = TRUE)))
targetDistMC <- distFromPos(sf::st_coordinates(sf::st_centroid(targetRanges[[3]],
byid = TRUE)))
```
## Start of simulations
*warning* this takes a long time to run.
```{r, eval = FALSE}
originRelAbund <- rep(1/3, 3)
nTargetSetups <- 5
nSims <- 2 #SET LOW FOR EXAMPLE
# nSims <- 200
nOriginSites = 3
targetPoints0 <- matrix(NA, 300, 2, dimnames = list(NULL, c("x", "y")))
a <- Sys.time()
output.sims <- vector("list", nTargetSetups)
for(target in 1:nTargetSetups){
sim.output <- data.frame(targetSetup = rep(NA,nSims),
sim = rep(NA,nSims),
MC.generated = rep(NA,nSims),
MC.realized = rep(NA,nSims),
MC.est = rep(NA,nSims),
MC.low = rep(NA,nSims),
MC.high = rep(NA,nSims),
rM.realized = rep(NA,nSims),
rM.est = rep(NA,nSims),
rM.low = rep(NA,nSims),
rM.high = rep(NA,nSims))
set.seed(9001)
targetSites <- targetRanges[[target]]
sf_use_s2(FALSE)
targetSites <- sf::st_make_valid(targetSites)
targetDist <- distFromPos(sf::st_coordinates(sf::st_centroid(targetSites,
byid = TRUE)))
# Extract simulated data
iso_dat <- data.frame(Site = rep(1:3,each = 100),
xcoords = c(sf::st_coordinates(Site1)[,1],
sf::st_coordinates(Site2)[,1],
sf::st_coordinates(Site3)[,1]),
ycoords = c(sf::st_coordinates(Site1)[,2],
sf::st_coordinates(Site2)[,2],
sf::st_coordinates(Site3)[,2]),
targetSite = unlist(unclass(sf::st_intersects(rbind(Site1,
Site2,
Site3),
targetSites))),
featherIso = terra::extract(featherIso,
terra::vect(rbind(Site1,
Site2,
Site3))))
iso_dat <- iso_dat[complete.cases(iso_dat),]
# generate transition data from simulation
sim_psi <- prop.table(table(iso_dat$Site,factor(iso_dat$targetSite,
1:nrow(targetSites))), 1)
sf_use_s2(TRUE)
MC.generated <- calcMC(originDist = originDist,
targetDist = targetDist,
originRelAbund = originRelAbund,
psi = sim_psi)
for (sim in 1:nSims) {
cat("Simulation Run", sim, "of", nSims, "for target",target,"at", date(), "\n")
sim_move <- simMove(rep(100, nOriginSites), originDist, targetDist, sim_psi, 1, 1)
originAssignment <- sim_move$animalLoc[,1,1,1]
targetAssignment <- sim_move$animalLoc[,2,1,1]
sf_use_s2(FALSE)
for (i in 1:300) {
targetPoint1 <- sf::st_sample(targetSites[targetAssignment[i],],
size = 1, type = "random", iter = 25)
targetPoints0[i,] <- sf::st_coordinates(targetPoint1)
}
targetPoints <- sf::st_as_sf(as.data.frame(targetPoints0), crs = 4326,
coords = c("x", "y"))
# Extract simulated data
iso_dat <- data.frame(Site = originAssignment,
xcoords = targetPoints0[,1],
ycoords = targetPoints0[,2],
targetSite = unlist(unclass(sf::st_intersects(targetPoints,
targetSites))),
featherIso = terra::extract(featherIso,
terra::vect(targetPoints)))
iso_dat <- iso_dat[complete.cases(iso_dat),]
# generate transition data from simulation
sim_psi0 <- table(iso_dat$Site,
factor(iso_dat$targetSite,
min(targetSites$Target):max(targetSites$Target)))
sim_psi_realized <- prop.table(sim_psi0, 1)
# get points ready for analysis
nSite1 <- table(iso_dat$Site)[1]
nSite2 <- table(iso_dat$Site)[2]
nSite3 <- table(iso_dat$Site)[3]
nTotal <- nSite1+nSite2+nSite3
originCap <- array(NA, c(nTotal,2))
wherecaught <- rep(paste0("Site", 1:3), c(nSite1, nSite2, nSite3))
originCap[which(pmatch(wherecaught,"Site1",dup = TRUE)==1),1] <- capCoords[1,1]
originCap[which(pmatch(wherecaught,"Site1",dup = TRUE)==1),2] <- capCoords[1,2]
originCap[which(pmatch(wherecaught,"Site2",dup = TRUE)==1),1] <- capCoords[2,1]
originCap[which(pmatch(wherecaught,"Site2",dup = TRUE)==1),2] <- capCoords[2,2]
originCap[which(pmatch(wherecaught,"Site3",dup = TRUE)==1),1] <- capCoords[3,1]
originCap[which(pmatch(wherecaught,"Site3",dup = TRUE)==1),2] <- capCoords[3,2]
originPoints <- sf::st_as_sf(as.data.frame(originCap), crs = 4326, coords = 1:2)
sf_use_s2(TRUE)
MC.realized <- calcMC(originDist = originDist,
targetDist = targetDist,
originRelAbund = originRelAbund,
psi = sim_psi_realized,
sampleSize=nTotal)
originPointDists <- distFromPos(originCap)
targetPointDists <- distFromPos(cbind(iso_dat$xcoords, iso_dat$ycoords))
simAssign <- isoAssign(isovalues = iso_dat$featherIso.GrowingSeasonD,
isoSTD = 12,
intercept = -17.57,
slope = 0.95,
odds = 0.67,
restrict2Likely = FALSE,
nSamples = 500,
sppShapefile = OVEN_single_poly,
relAbund = relativeAbund,
verbose = 2,
isoWeight = -0.7,
abundWeight = 0,
assignExtent = c(-179,-60,15,89),
element = "Hydrogen",
period = "GrowingSeason")
psi <- estTransition(targetRaster = simAssign,
targetSites = targetSites,
originPoints = originPoints,
originSites = originSites, isRaster = TRUE,
nSamples = 100, nSim = 5, verbose = 0)
rM <- estMantel(targetRaster = simAssign,
targetSites = targetSites,
originPoints = originPoints,
isGL = FALSE, isTelemetry = FALSE,
originSites = originSites, isRaster = TRUE,
nBoot = 100, nSim = 5, verbose = 0, captured = "origin")
simEst <- estStrength(originRelAbund = originRelAbund,
targetDist = targetDist,
psi = psi,
originDist = originDist,
nSamples = 100,
verbose = 0,
alpha = 0.05)
sim.output$targetSetup[sim] <- target
sim.output$sim[sim]<-sim
sim.output$MC.generated[sim] <- MC.generated
sim.output$MC.realized[sim] <- MC.realized
sim.output$MC.est[sim] <- simEst$MC$mean
sim.output$MC.low[sim] <- simEst$MC$bcCI[1]
sim.output$MC.high[sim] <- simEst$MC$bcCI[2]
sim.output$rM.realized[sim] <- calcMantel(originDist = originPointDists,
targetDist = targetPointDists)$pointCorr
sim.output$rM.est[sim] <- rM$corr$mean
sim.output$rM.low[sim] <- rM$corr$bcCI[1]
sim.output$rM.high[sim] <- rM$corr$bcCI[2]
}
output.sims[[target]] <- sim.output
}
Sys.time()-a
output.sims <- do.call("rbind", output.sims)
#
```
Summarize the output
```{r, eval = FALSE}
sim.output <- transform(output.sims,
MC.generated.cover = as.integer((MC.low <= MC.generated &
MC.high >= MC.generated)),
MC.realized.cover = as.integer((MC.low <= MC.realized &
MC.high >= MC.realized)),
MC.generated.error = MC.est - MC.generated,
MC.realized.error = MC.est - MC.realized,
rM.cover = as.integer((rM.low <= rM.realized &
rM.high >= rM.realized)),
rM.error = rM.est - rM.realized)
summary(sim.output)
# Examine results
aggregate(MC.generated.error ~ targetSetup, sim.output, mean)
aggregate(MC.generated.error ~ targetSetup, sim.output, function (x) mean(abs(x)))
aggregate(MC.generated.cover ~ targetSetup, sim.output, mean)
aggregate(MC.realized.error ~ targetSetup, sim.output, mean)
aggregate(MC.realized.error ~ targetSetup, sim.output, function (x) mean(abs(x)))
aggregate(MC.realized.cover ~ targetSetup, sim.output, mean)
aggregate(I(MC.realized - MC.generated) ~ targetSetup, sim.output, mean)
aggregate(rM.error ~ targetSetup, sim.output, mean)
aggregate(rM.error ~ targetSetup, sim.output, function (x) mean(abs(x)))
aggregate(rM.cover ~ targetSetup, sim.output, mean)
aggregate(MC.est ~ targetSetup, sim.output, mean)
```