mrds (version 2.3.0)

stake77: Wooden stake data from 1977 survey

Description

Multiple surveys by different observers of a single 1km transect containing 150 wooden stakes placed randomly throughout a 40 m strip (20m on either side).

Format

A data frame with 150 observations on the following 10 variables.

StakeNo

unique number for each stake 1-150

PD

perpendicular distance at which the stake was placed from the line

Obs1

0/1 whether missed/seen by observer 1

Obs2

0/1 whether missed/seen by observer 2

Obs3

0/1 whether missed/seen by observer 3

Obs4

0/1 whether missed/seen by observer 4

Obs5

0/1 whether missed/seen by observer 5

Obs6

0/1 whether missed/seen by observer 6

Obs7

0/1 whether missed/seen by observer 7

Obs8

0/1 whether missed/seen by observer 8

References

Burnham, K. P., D. R. Anderson, and J. L. Laake. 1980. Estimation of Density from Line Transect Sampling of Biological Populations. Wildlife Monographs:7-202.

Examples

# \donttest{
data(stake77)
# Extract functions for stake data and put in the mrds format
extract.stake <- function(stake,obs){
  extract.obs <- function(obs){
    example <- subset(stake,eval(parse(text=paste("Obs",obs,"==1",sep=""))),
                      select="PD")
    example$distance <- example$PD
    example$object <- 1:nrow(example)
    example$PD <- NULL
    return(example)
  }
  if(obs!="all"){
    return(extract.obs(obs=obs))
  }else{
    example <- NULL
    for(i in 1:(ncol(stake)-2)){
      df <- extract.obs(obs=i)
      df$person <- i
      example <- rbind(example,df)
    }
    example$person <- factor(example$person)
    example$object <- 1:nrow(example)
    return(example)
  }
}
extract.stake.pairs <- function(stake,obs1,obs2,removal=FALSE){
  obs1 <- paste("Obs",obs1,sep="")
  obs2 <- paste("Obs",obs2,sep="")
  example <- subset(stake,eval(parse(text=paste(obs1,"==1 |",obs2,"==1 ",
                                       sep=""))),select=c("PD",obs1,obs2))
  names(example) <- c("distance","obs1","obs2")
  detected <- c(example$obs1,example$obs2)
  example <- data.frame(object   = rep(1:nrow(example),2),
                        distance = rep(example$distance,2),
                        detected = detected,
                        observer = c(rep(1,nrow(example)),
                                     rep(2,nrow(example))))
  if(removal) example$detected[example$observer==2] <- 1
  return(example)
}
# extract data for observer 1 and fit a single observer model
stakes <- extract.stake(stake77,1)
ds.model <- ddf(dsmodel = ~mcds(key = "hn", formula = ~1), data = stakes,
                method = "ds", meta.data = list(width = 20))
plot(ds.model,breaks=seq(0,20,2),showpoints=TRUE)
ddf.gof(ds.model)

# extract data from observers 1 and 3 and fit an io model
stkpairs <- extract.stake.pairs(stake77,1,3,removal=FALSE)
io.model <- ddf(dsmodel = ~mcds(key = "hn", formula=~1),
                mrmodel=~glm(formula=~distance),
                data = stkpairs, method = "io")
summary(io.model)
par(mfrow=c(3,2))
plot(io.model,breaks=seq(0,20,2),showpoints=TRUE,new=FALSE)
dev.new()
ddf.gof(io.model)
# }