In umd-lib/animalmove: Analysis of animal population-level movement patterns

Realized Mobility Index

library(knitr)
opts_chunk$set(out.extra='style="display:block; margin: auto"', fig.align="center")

Load package library

library(lubridate)
library(animalmove)
library(plyr)

Subsample Data

Buffalo dataset has been saved in the package data directory , and loaded on the package load.

Raw buffalo dataset contains unaltered original data.

data(buffalo)
head(buffalo)

nrow(buffalo)

currentnames <- colnames(buffalo)
currentnames

names(buffalo)[names(buffalo)=="timestamp"] <- "time"
names(buffalo)[names(buffalo)=="utm.easting"] <- "x"
names(buffalo)[names(buffalo)=="utm.northing"] <- "y"
names(buffalo)[names(buffalo)=="tag.local.identifier"] <- "id"
names(buffalo)[names(buffalo)=="individual.taxon.canonical.name"] <- "pop.type"

# Data Conversion
buffalo$time <- as.POSIXct(strptime(buffalo$time,format="%Y-%m-%d %H:%M",tz="GMT"))

#Display new names
newnames <- colnames(buffalo)
newnames
head(buffalo)

Number of rows in the buffalo data & data set structure

length(table((buffalo$id)))

str(buffalo)

Subsample data within time interval

---

We select at most 6 individuals within 2009, time interval 50 hours, and accuracy 50 hours, and subsampling scheme for Realized Mobility Index

rmi.subsample.data <- subsample(dat=buffalo, start=c("2005-02-17 00:00:00"),end="2006-12-31 00:00:00",interval=c("48 hours"),accuracy=c("3 hours"),minIndiv=3,maxIndiv=6,mustIndiv=NULL,index.type="rmi")

buffalo.indiv <- Individuals(rmi.subsample.data, id="id", time="time", x="x", y="y", group.by="pop.type", proj4string= CRS("+proj=utm +zone=28 +datum=WGS84"))

head(coordinates(buffalo.indiv))
bbox(buffalo.indiv)
head(show(buffalo.indiv),2)
head(SpatialPoints(buffalo.indiv), 2)
coordnames(buffalo.indiv)

buffalo.data.attr <- as.data.frame(buffalo.indiv)
head(buffalo.data.attr)

buffalo.individual.mcp <- mcp(buffalo.indiv[,"id"], percent = 100)
buffalo.individual.mcp

buffalo.population.mcp <- mcp.population(buffalo.indiv, percent = 100)
buffalo.population.mcp

show.mcp(buffalo.indiv, percent = 100, id="id")
print(buffalo.indiv)

Note, a number of rows in the rmi subsample dataset

nrow(rmi.subsample.data)

Analysis

Compute Realized Mobility Index

---

fg.pal <- color.palette(length(unique(buffalo.data.attr$pop.type)))
bg.pal <- color.palette(length(unique(buffalo.data.attr$pop.type)), palette = c("Dark2"))  

plot(buffalo.individual.mcp, col=fg.pal)
plot(buffalo.indiv, col="green")

rmi.index.population <- rmi.index(buffalo.indiv, percent = 100, id = "id")

plot(rmi.index.population)

RMI Data

rmi.index.population

RMI Summary

---

rmi.index.population
summary(rmi.index.population)

Plot Results

---

plot(rmi.index.population)

umd-lib/animalmove documentation built on May 3, 2019, 2:24 p.m.