Organize data for the multinomial-Poisson mixture model of Royle (2004) fit by multinomPois
Organizes count data along with the covariates.
This S4 class is required by the data argument of
multinomPois
unmarkedFrameMPois(y, siteCovs=NULL, obsCovs=NULL, type, obsToY,
mapInfo, piFun)y |
An RxJ matrix of count data, where R is the number of sites (transects) and J is the maximum number of observations per site. |
siteCovs |
A |
obsCovs |
Either a named list of RxJ |
type |
Either "removal" for removal sampling, "double" for standard
double observer sampling, or "depDouble" for dependent double observer
sampling. If this argument not specified, the user must
provide an |
obsToY |
A matrix describing the relationship between |
mapInfo |
Currently ignored |
piFun |
Function used to compute the multinomial cell probabilities
from a matrix of detection probabilities. This is created automatically
if |
unmarkedFrameMPois is the S4 class that holds data to be passed
to the multinomPois model-fitting function.
an object of class unmarkedFrameMPois
Royle, J. A. (2004). Generalized estimators of avian abundance from count survey data. Animal Biodiversity and Conservation, 27(1), 375-386.
# Fake doulbe observer data
R <- 4 # number of sites
J <- 2 # number of observers
y <- matrix(c(
1,0,3,
0,0,0,
2,0,1,
0,0,2), nrow=R, ncol=J+1, byrow=TRUE)
y
site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
site.covs
obs.covs <- list(
x3 = matrix(c(
-1,0,
-2,0,
-3,1,
0,0),
nrow=R, ncol=J, byrow=TRUE),
x4 = matrix(c(
'a','b',
'a','b',
'a','b',
'a','b'),
nrow=R, ncol=J, byrow=TRUE))
obs.covs
# Create unmarkedFrame
umf <- unmarkedFrameMPois(y=y, siteCovs=site.covs, obsCovs=obs.covs,
type="double")
# The above is the same as:
o2y <- matrix(1, 2, 3)
pifun <- function(p)
{
M <- nrow(p)
pi <- matrix(NA, M, 3)
pi[, 1] <- p[, 1] * (1 - p[, 2])
pi[, 2] <- p[, 2] * (1 - p[, 1])
pi[, 3] <- p[, 1] * p[, 2]
return(pi)
}
umf <- unmarkedFrameMPois(y=y, siteCovs=site.covs, obsCovs=obs.covs,
obsToY=o2y, piFun="pifun")
# Fit a model
fm <- multinomPois(~1 ~1, umf)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.