Occupancy Single Season | R Documentation |
Functions to estimate occupancy from detection/non-detection data for a single season. occSS
is the general-purpose function, and occSStime
provides plots of detection probability against time. occSS0
and occSScovSite
are faster functions for simpler models with summarized data. See occSSrn
for the Royle-Nichols model for abundance-induced heterogeneity in detection probability.
occSS(DH, model=NULL, data = NULL, ci=0.95, link=c("logit", "probit"), verify=TRUE, ...) occSStime(DH, model=p~1, data=NULL, ci=0.95, plot=TRUE, link=c("logit", "probit"), verify=TRUE, ...) occSS0(y, n, ci=0.95, link=c("logit", "probit"), ...) occSScovSite(y, n, model=NULL, data = NULL, ci=0.95, link=c("logit", "probit"), ...)
DH |
a 1/0/NA matrix (or data frame) of detection histories, sites x occasions. |
model |
a list of formulae symbolically defining a linear predictor for each parameter in terms of covariates. If NULL, an intercept-only model is used, ie, psi(.) p(.). |
ci |
the confidence interval to use. |
data |
a data frame containing the variables in the model. For |
link |
the link function to use, either logit or probit; see Links. |
verify |
if TRUE, the data provided will be checked. |
plot |
if TRUE (default), draws a plot of probability of detection vs time. |
y |
a vector with the number of detections at each site. |
n |
a scalar or vector with the number of visits (survey occasions) at each site. |
... |
other arguments passed to |
occSS
allows for psi or p to be modelled as a logistic or probit function of site covariates or survey covariates, as specified by model
. It includes a built in .time
covariate which can be used for modelling p with time as a fixed effect, and .Time, .Time2, .Time3
for a linear, quadratic or cubic trend. A built-in .b
covariate corresponds to a behavioural effect, where detection depends on whether the species was detected on the previous occasion or not.
occSStime
allows for time-varying covariates that are the same across all sites, eg, moon-phase. Time variables are built in, as for occSS
. A plot of detection probability vs time is produced if plot=TRUE
.
occSS0
implements a simple model with one parameter for probability of occupancy and one for probability of detection, ie. a psi(.) p(.)
model.
occSScovSite
allows for site covariates but not for occasion or survey covariates.
Numeric covariates in data
are standardised to facilitate convergence. This applies to binary covariates coded as 1/0; if this is not what you want, code these as TRUE/FALSE or as factors.
For speed, use the simplest function which will cope with your model. For example, you can run psi(.) p(.) models in occSScovSite
or occSS
, but occSS0
is much faster.
Returns an object of class wiqid
, see wiqid-class for details.
Output has been checked against output from PRESENCE (Hines 2006) v.5.5 for the salamanders
and weta
data sets. Real values are mostly the same to 4 decimal places, though there is occasionally a discrepancy of 0.0001. AICs are the same.
Mike Meredith
MacKenzie, D I; J D Nichols; G B Lachman; S Droege; J A Royle; C A Langtimm. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83:2248-2255.
MacKenzie, D I; J D Nichols; A J Royle; K H Pollock; L L Bailey; J E Hines 2006. Occupancy Estimation and Modeling : Inferring Patterns and Dynamics of Species Occurrence. Elsevier Publishing.
Hines, J. E. (2006). PRESENCE - Software to estimate patch occupancy and related parameters. SGS-PWRC. http://www.mbr-pwrc.usgs.gov/software/presence.html.
See the examples for the weta
data set. See occ2sps
for single-season two-species models and occMS
for multi-season models.
# The blue ridge salamanders data from MacKenzie et al (2006) p99: data(salamanders) occSS(salamanders) occSStime(salamanders, p ~ .time) # time as a fixed effect occSStime(salamanders, p ~ .Time + .Time2) # a quadratic time effect occSS(salamanders, p ~ .b) # or use the fast functions with y, n format: y <- rowSums(salamanders) n <- rowSums(!is.na(salamanders)) occSS0(y, n) occSScovSite(y, n)
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