Hello,
This should be a relatively simple question but I have been struggling with it. I have a capthist object with 4 different sessions (each composed of 7 occasions), imported as required using a vector of trapfiles (one for each session):
RSData<-read.capthist(captfile="RSdata_LoggedForest.txt",trapfile=c("E1_RSTrapdata_Session1.txt","E2_RSTrapdata_Session2.txt","F1_RSTrapdata_Session3.txt","F2_RSTrapdata_Session4.txt"),detector="single")
When I inspect my data (summary) everything seems to be fine and all the sessions have been appropriately specified. However, when I try and run a simple model looking at density as a function of session, secr.fit returns the following output:
>RSsecr<-secr.fit(RSData,model=list(D~session,g0~1,sigma~1))
>RSsecr
secr.fit( capthist = RSData, model = list(D ~ session, g0 ~ 1, sigma ~ 1),
buffer = 50 )
secr 2.1.0, 15:47:17 07 Aug 2011
$`1`
Object class traps
Detector type single
Detector number 96
Average spacing 6.546681 m
x-range 876193.7 876324.4 m
y-range 521046.5 521316.3 m
$`2`
Object class traps
Detector type single
Detector number 96
Average spacing 7.640513 m
x-range 876302 876435 m
y-range 521490.1 521759.1 m
$`3`
Object class traps
Detector type single
Detector number 96
Average spacing 8.101695 m
x-range 871723.2 871813.8 m
y-range 520921.8 521185.1 m
$`4`
Object class traps
Detector type single
Detector number 96
Average spacing 7.708401 m
x-range 871764.1 871861 m
y-range 520466.6 520731 m
1 2 3 4
Occasions 7 7 7 7
Detections 72 57 78 57
Animals 29 26 36 28
Detectors 96 96 96 96
Model : D~session g0~1 sigma~1
Fixed (real) : none
Detection fn : halfnormal
Distribution : poisson
N parameters : 6
Log likelihood : -1e+10
AIC : 2e+10
AICc : 2e+10
Beta parameters (coefficients)
beta SE.beta lcl ucl
D 2.255436 NA NA NA
D.session2 0.000000 NA NA NA
D.session3 0.000000 NA NA NA
D.session4 0.000000 NA NA NA
g0 -1.714053 NA NA NA
sigma 2.494075 NA NA NA
Variance-covariance matrix of beta parameters
NULL
Fitted (real) parameters evaluated at base levels of covariates
session = 1
link estimate SE.estimate lcl ucl
D log 9.5394563 NA NA NA
g0 logit 0.1526388 NA NA NA
sigma log 12.1105241 NA NA NA
session = 2
link estimate SE.estimate lcl ucl
D log 9.5394563 NA NA NA
g0 logit 0.1526388 NA NA NA
sigma log 12.1105241 NA NA NA
session = 3
link estimate SE.estimate lcl ucl
D log 9.5394563 NA NA NA
g0 logit 0.1526388 NA NA NA
sigma log 12.1105241 NA NA NA
session = 4
link estimate SE.estimate lcl ucl
D log 9.5394563 NA NA NA
g0 logit 0.1526388 NA NA NA
sigma log 12.1105241 NA NA NA
It seems secr.fit is unable to estimate loglik properly and only considers the first session, even though it acknowledges the existence of 4 distinct sessions.
If someone could point out what I am doing wrong it would be really helpful! Sorry if this is obvious.
Many thanks!
Jeremy