constructor of unmarkedFitList objects

Organize models for model selection or model-averaged prediction.

fitList(..., fits)

Arguments

...	Fitted models. Preferrably named.
fits	An alternative way of providing the models. A (preferrably named) list of fitted models.

Note

Two requirements exist to conduct AIC-based model-selection and model-averaging in unmarked. First, the data objects (ie, unmarkedFrames) must be identical among fitted models. Second, the response matrix must be identical among fitted models after missing values have been removed. This means that if a response value was removed in one model due to missingness, it needs to be removed from all models.

Author

Richard Chandler rbchan@uga.edu

Examples

data(linetran)
(dbreaksLine <- c(0, 5, 10, 15, 20)) 
#> [1]  0  5 10 15 20
lengths <- linetran$Length * 1000

ltUMF <- with(linetran, {
  unmarkedFrameDS(y = cbind(dc1, dc2, dc3, dc4), 
  siteCovs = data.frame(Length, area, habitat), dist.breaks = dbreaksLine,
  tlength = lengths, survey = "line", unitsIn = "m")
  })

fm1 <- distsamp(~ 1 ~1, ltUMF)
fm2 <- distsamp(~ area ~1, ltUMF)
fm3 <- distsamp( ~ 1 ~area, ltUMF)

## Two methods of creating an unmarkedFitList using fitList()

# Method 1
fmList <- fitList(Null=fm1, .area=fm2, area.=fm3)

# Method 2. Note that the arugment name "fits" must be included in call.
models <- list(Null=fm1, .area=fm2, area.=fm3)
fmList <- fitList(fits = models)

# Extract coefficients and standard errors
coef(fmList)
#>         lam(Int)   p(Int)   p(area)   lam(area)
#> Null  -0.1710554 2.386380        NA          NA
#> .area -0.1678270 3.002507 -0.120364          NA
#> area.  0.2364320 2.386386        NA -0.08005895
SE(fmList)
#>        lam(Int)    p(Int)    p(area) lam(area)
#> Null  0.1337819 0.1273598         NA        NA
#> .area 0.1340212 0.5401575 0.09548038        NA
#> area. 0.5122837 0.1273614         NA 0.0979427

# Model-averaged prediction
predict(fmList, type="state")
#>    Predicted        SE     lower    upper
#> 1  0.8312132 0.1182056 0.6325438 1.092772
#> 2  0.8524076 0.1169823 0.6528972 1.112951
#> 3  0.8331920 0.1166589 0.6358157 1.092103
#> 4  0.8315502 0.1179278 0.6331133 1.092628
#> 5  0.8444727 0.1130560 0.6495892 1.097823
#> 6  0.8628921 0.1284214 0.6509868 1.145233
#> 7  0.8625919 0.1280257 0.6511054 1.144148
#> 8  0.8271520 0.1219457 0.6253753 1.095368
#> 9  0.8195735 0.1303255 0.6112124 1.103804
#> 10 0.8555768 0.1198427 0.6529052 1.121399
#> 11 0.8164013 0.1341851 0.6052469 1.108477
#> 12 0.8488432 0.1145846 0.6520535 1.105031

# Model selection
modSel(fmList, nullmod="Null")
#>       nPars    AIC delta AICwt cumltvWt   Rsq
#> Null      2 164.75  0.00  0.43     0.43 0.000
#> .area     3 165.18  0.43  0.35     0.78 0.122
#> area.     3 166.08  1.32  0.22     1.00 0.055