# Create an object of class unmarkedFramePCO that contains data used by pcountOpen. 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` ```r unmarkedFramePCO(y, siteCovs=NULL, obsCovs=NULL, yearlySiteCovs, 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. - `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 . ## Returns an object of class unmarkedFramePCO ## See Also `unmarkedFrame-class`, `unmarkedFrame`, `pcountOpen` ## Examples ```r # 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) ```

unmarkedFramePCO function