This function extracts various summary statistics from time to detection
data of various unmarkedFrame and unmarkedFit classes.
detTime(object, plot.time = TRUE, plot.seasons = FALSE,
cex.axis = 1, cex.lab = 1, cex.main = 1, ...)# S3 method for unmarkedFrameOccuTTD
detTime(object, plot.time = TRUE,
plot.seasons = FALSE, cex.axis = 1, cex.lab = 1,
cex.main = 1, ...)
# S3 method for unmarkedFitOccuTTD
detTime(object, plot.time = TRUE,
plot.seasons = FALSE, cex.axis = 1, cex.lab = 1,
cex.main = 1, ...)
detTime returns a list with the following components:
a table with the quantiles of time to detection data pooled across seasons, but excluding censored observations.
a list of tables with the quantiles of season-specific time to detection data, but excluding censored observations.
a matrix where the rows correspond to each sampling
season and where columns consist of the number of sites sampled in
season \(t\) (sampled) and the number of sites with at
least one detection in season \(t\) (detected). For
multiseason data, the matrix includes the number of sites sampled in
season \(t - 1\) with colonizations observed in season \(t\)
(colonized), the number of sites sampled in season \(t -
1\) with extinctions observed in season \(t\) (extinct), the
number of sites sampled in season \(t - 1\) without changes
observed in season \(t\) (static), and the number of sites
sampled in season \(t\) that were also sampled in season \(t -
1\) (common).
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 (naive.occ). For
multiseason data, the matrix includes the proportion of sites
sampled in season \(t - 1\) with colonizations observed in season
\(t\) (naive.colonization), the proportion of sites
sampled in season \(t - 1\) with extinctions observed in season
\(t\) (naive.extinction), and the proportion of sites
sampled in season \(t - 1\) with no changes observed in season
\(t\).
the number of seasons (primary periods) in the data set.
the maximum number of visits per season in the data set.
logical vector indicating whether data were
collected or not during a given season (primary period), where
TRUE indicates that no data were collected during the season.
an object of various unmarkedFrame or unmarkedFit
classes containing time to detection data.
logical. Specifies if the time to detection data (pooled across seasons) should be plotted.
logical. Specifies if the time to detection data should be plotted for each season separately. This argument is only relevant for data collected across more than a single season.
expansion factor influencing the size of axis annotations on plots produced by the function.
expansion factor influencing the size of axis labels on plots produced by the function.
expansion factor influencing the size of the main title above plots produced by the function.
additional arguments passed to the function.
Marc J. Mazerolle
This function computes a number of summary statistics in data sets used for the time to detection models of Garrard et al. (2008, 2013).
detTime can take data frames of the unmarkedFrameOccuTTD
class as input, or can also extract the raw data from model objects of
the unmarkedFitOccuTTD class. Note that different model
objects using the same data set will have identical values.
Garrard, G. E., Bekessy, S. A., McCarthy, M. A., Wintle, B. A. (2008) When have we looked hard enough? A novel method for setting minimum survey effort protocols for flora surveys. Austral Ecology 33, 986--998.
Garrard, G. E., McCarthy, M. A., Williams, N. S., Bekessy, S. A., Wintle, B. A. (2013) A general model of detectability using species traits. Methods in Ecology and Evolution 4, 45--52.
countDist, countHist, detHist,
Nmix.chisq, Nmix.gof.test