unmarked: unmarkedFramePCO – R documentation

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unmarkedFramePCO

Create an object of class unmarkedFramePCO that contains data used by pcountOpen.

Description

Organizes repeated count data along with the covariates and possibly the dates on which each survey was conducted. This S4 class is required by the data argument of pcountOpen

Usage

unmarkedFramePCO(y, siteCovs=NULL, obsCovs=NULL, yearlySiteCovs, mapInfo,
    numPrimary, primaryPeriod)

Arguments

`y`	An MxJT matrix of the repeated count data, where M is the number of sites, J is the maximum number of secondary sampling periods per site and T is the maximum number of primary sampling periods per site.
`siteCovs`	A `data.frame` of covariates that vary at the site level. This should have M rows and one column per covariate
`obsCovs`	Either a named list of `data.frame`s of covariates that vary within sites, or a `data.frame` with MxJT rows in site-major order.
`yearlySiteCovs`	Either a named list of MxT `data.frame`s, or a site-major `data.frame` with MT rows and 1 column per covariate.
`mapInfo`	Currently ignored
`numPrimary`	Maximum number of observed primary periods for each site
`primaryPeriod`	matrix of integers indicating the primary period of each survey.

Details

unmarkedFramePCO is the S4 class that holds data to be passed to the pcountOpen model-fitting function.

The unmarkedFramePCO class is similar to the unmarkedFramePCount class except that it contains the dates for each survey, which needs to be supplied .

Value

an object of class unmarkedFramePCO

Examples

# 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)

unmarked

Models for Data from Unmarked Animals

v1.1.0

GPL (>= 3)

Authors

Richard Chandler [aut], Ken Kellner [aut], Ian Fiske [aut], David Miller [aut], Andy Royle [cre, aut], Jeff Hostetler [aut], Rebecca Hutchinson [aut], Adam Smith [aut], Marc Kery [ctb], Mike Meredith [ctb], Auriel Fournier [ctb], Ariel Muldoon [ctb], Chris Baker [ctb]

Initial release

2021-05-05