countHist {AICcmodavg}  R Documentation 
Compute Summary Statistics from Count Histories
Description
This function extracts various summary statistics from count data of
various unmarkedFrame
and unmarkedFit
classes.
Usage
countHist(object, plot.freq = TRUE, cex.axis = 1, cex.lab = 1,
cex.main = 1, ...)
## S3 method for class 'unmarkedFramePCount'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1, ...)
## S3 method for class 'unmarkedFitPCount'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1, ...)
## S3 method for class 'unmarkedFrameGPC'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1, ...)
## S3 method for class 'unmarkedFitGPC'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1, ...)
## S3 method for class 'unmarkedFrameMPois'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1, ...)
## S3 method for class 'unmarkedFitMPois'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1, ...)
## S3 method for class 'unmarkedFramePCO'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1,
plot.seasons = FALSE, ...)
## S3 method for class 'unmarkedFitPCO'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1,
plot.seasons = FALSE, ...)
## S3 method for class 'unmarkedFrameGMM'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1,
plot.seasons = FALSE, ...)
## S3 method for class 'unmarkedFitGMM'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1,
plot.seasons = FALSE, ...)
## S3 method for class 'unmarkedFrameMMO'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1,
plot.seasons = FALSE, ...)
## S3 method for class 'unmarkedFitMMO'
countHist(object, plot.freq = TRUE,
cex.axis = 1, cex.lab = 1, cex.main = 1,
plot.seasons = FALSE, ...)
Arguments
object 
an object of various 
plot.freq 
logical. Specifies if the count data (pooled across seasons) should be plotted. 
cex.axis 
expansion factor influencing the size of axis annotations on plots produced by the function. 
cex.lab 
expansion factor influencing the size of axis labels on plots produced by the function. 
cex.main 
expansion factor influencing the size of the main title above plots produced by the function. 
plot.seasons 
logical. Specifies if the count data should be plotted for each season separately. This argument is only relevant for data collected across more than a single season. 
... 
additional arguments passed to the function. 
Details
This function computes a number of summary statistics in data sets used for various Nmixture models including those of Royle (2004a, b), Dail and Madsen (2011), and Chandler et al. (2011).
countHist
can take data frames of the
unmarkedFramePCount
, unmarkedFrameGPC
,
unmarkedFrameMPois
, unmarkedFramePCO
,
unmarkedFrameGMM
, unmarkedFrameMMO
classes as input.
For convenience, the function can also extract the raw data from model
objects of classes unmarkedFitPCount
, unmarkedFitGPC
,
unmarkedFitMPois
, unmarkedFitPCO
, unmarkedFitGMM
,
and unmarkedFitMMO
. Note that different model objects using the
same data set will have identical values.
Value
countHist
returns a list with the following components:
count.table.full 
a table with the frequency of each observed count. 
count.table.seasons 
a list of tables with the frequency of each seasonspecific count. 
hist.table.full 
a table with the frequency of each count history across the entire sampling period. 
hist.table.seasons 
a list of tables with the frequency of each count history for each primary period (season). 
out.freqs 
a matrix where the rows correspond to each sampling
season and where columns consist of the number of sites sampled in
season 
out.props 
a matrix where the rows correspond to each sampling
season and where columns consist of the proportion of sites in
season t with at least one detection ( 
n.seasons 
the number of seasons (primary periods) in the data set. 
n.visits.season 
the maximum number of visits per season in the data set. 
missing.seasons 
logical vector indicating whether data were
collected or not during a given season (primary period), where

Author(s)
Marc J. Mazerolle
References
Chandler, R. B., Royle, J. A., King, D. I. (2011) Inference about density and temporary emigration in unmarked populations. Ecology 92, 1429–1435.
Dail, D., Madsen, L. (2011) Models for estimating abundance from repeated counts of an open population. Biometrics 67, 577–587.
Royle, J. A. (2004a) Nmixture models for estimating population size from spatially replicated counts. Biometrics 60, 108–115.
Royle, J. A. (2004b) Generalized estimators of avian abundance from count survey data. Animal Biodiversity and Conservation 27, 375–386.
See Also
covDiag
, detHist
, detTime
,
countDist
, Nmix.chisq
,
Nmix.gof.test
Examples
##modified example from ?pcount
## Not run:
if(require(unmarked)){
data(mallard)
mallardUMF < unmarkedFramePCount(mallard.y, siteCovs = mallard.site,
obsCovs = mallard.obs)
##compute descriptive stats from data object
countHist(mallardUMF)
##run single season model
fm.mallard < pcount(~ ivel+ date + I(date^2) ~ length + elev +
forest, mallardUMF, K=30)
##compute descriptive stats from model object
countHist(fm.mallard)
}
## End(Not run)