# Repeated count data with 5 primary periods and
# no secondary sampling periods (ie J==1)
y1 <- matrix(c(
0, 2, 3, 2, 0,
2, 2, 3, 1, 1,
1, 1, 0, 0, 3,
0, 0, 0, 0, 0), nrow=4, ncol=5, byrow=TRUE)
# Site-specific covariates
sc1 <- data.frame(x1 = 1:4, x2 = c('A','A','B','B'))
# Observation-specific covariates
oc1 <- list(
x3 = matrix(1:5, nrow=4, ncol=5, byrow=TRUE),
x4 = matrix(letters[1:5], nrow=4, ncol=5, byrow=TRUE))
# Primary periods of surveys
primaryPeriod1 <- matrix(as.integer(c(
1, 2, 5, 7, 8,
1, 2, 3, 4, 5,
1, 2, 4, 5, 6,
1, 3, 5, 6, 7)), nrow=4, ncol=5, byrow=TRUE)
# Create the unmarkedFrame
umf1 <- unmarkedFramePCO(y=y1, siteCovs=sc1, obsCovs=oc1, numPrimary=5,
primaryPeriod=primaryPeriod1)
# Take a look
umf1
summary(umf1)
# Repeated count data with 4 primary periods and
# no 2 secondary sampling periods (ie J=2)
y2 <- matrix(c(
0,0, 2,2, 3,2, 2,2,
2,2, 2,1, 3,2, 1,1,
1,0, 1,1, 0,0, 0,0,
0,0, 0,0, 0,0, 0,0), nrow=4, ncol=8, byrow=TRUE)
# Site-specific covariates
sc2 <- data.frame(x1 = 1:4, x2 = c('A','A','B','B'))
# Observation-specific covariates
oc2 <- list(
x3 = matrix(1:8, nrow=4, ncol=8, byrow=TRUE),
x4 = matrix(letters[1:8], nrow=4, ncol=8, byrow=TRUE))
# Yearly-site covariates
ysc <- list(
x5 = matrix(c(
1,2,3,4,
1,2,3,4,
1,2,3,4,
1,2,3,4), nrow=4, ncol=4, byrow=TRUE))
# Primary periods of surveys
primaryPeriod2 <- matrix(as.integer(c(
1,2,5,7,
1,2,3,4,
1,2,4,5,
1,3,5,6)), nrow=4, ncol=4, byrow=TRUE)
# Create the unmarkedFrame
umf2 <- unmarkedFramePCO(y=y2, siteCovs=sc2, obsCovs=oc2,
yearlySiteCovs=ysc,
numPrimary=4, primaryPeriod=primaryPeriod2)
# Take a look
umf2
summary(umf2)
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