These examples take 1-2 minutes to run
We will use [run.mar()] arguments to set variables and restrictions. See the [run.mar()] page for information. No restrictions on the restriction matrix (all 0.5).
data(L4.mar)
myvar <- c(0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 2, 2, 2) # 8 variates, 3 covariates
myres <- matrix(0.5,
nrow = length(which(myvar == 1)),
ncol = length(which(myvar != 0))
)Fit a MAR1 model first.
run1 <- run.mar(L4.mar, variables = myvar, restrictions = myres, search = "exhaustive")
#>
#>
#> searching for best-fit model...
#> ...BEST-FIT MODEL SELECTED
#> ( search time: 0 minutes 1 seconds )
#>
#>
#>
#> identifying 10 lowest AIC models...
#> ...TOP MODELS RETAINED
#>
#>
#>
#> bootstrapping best-fit model...
#> ...BOOTSTRAPPING COMPLETE
#>
#>
#> ════════════════════════════════════════════════════════════════════════════════
#>
#> This allows use to include observation error. control
can be passed in to limit the number of iterations run.
ss.fit$B
#> amphipod chaetognath cladoceran calanoid.lg calanoid.sm
#> amphipod 0.2495807 0.00000000 0.0000000 0.2087382 0.0000000
#> chaetognath 0.0000000 0.55938796 0.0000000 0.0000000 -0.1009282
#> cladoceran 0.0000000 0.00000000 0.4927539 0.0000000 0.0000000
#> calanoid.lg -0.4781403 -0.01429697 -0.1894227 0.6181397 0.0000000
#> calanoid.sm -0.3381246 0.00000000 0.0000000 0.1029780 0.4478054
#> cyclopoid 0.0000000 0.00000000 0.0000000 0.0000000 0.0000000
#> diatom 0.0000000 0.00000000 0.0000000 -0.2615612 0.0000000
#> dino 0.3528929 0.00000000 -0.2273365 -0.1961949 0.4100545
#> cyclopoid diatom dino
#> amphipod -0.1234572 0.148922126 0.00000000
#> chaetognath 0.0000000 0.000000000 0.00000000
#> cladoceran 0.0000000 0.000000000 0.00000000
#> calanoid.lg -0.1680414 -0.007289215 0.00000000
#> calanoid.sm 0.0000000 -0.017631458 -0.07566676
#> cyclopoid 0.6143973 0.000000000 0.00000000
#> diatom 0.0000000 0.276714637 0.00000000
#> dino -0.4087143 0.000000000 0.21599674
run1$bestfit$B
#> amphipod chaetognath cladoceran calanoid.lg calanoid.sm
#> amphipod 0.08151863 0.00000000 0.0000000 0.23997271 0.0000000
#> chaetognath 0.00000000 0.48254589 0.0000000 0.00000000 -0.1039079
#> cladoceran 0.00000000 0.00000000 0.4150929 0.00000000 0.0000000
#> calanoid.lg -0.29967953 0.01557868 -0.1365731 0.42833032 0.0000000
#> calanoid.sm -0.26909543 0.00000000 0.0000000 0.10679836 0.3410686
#> cyclopoid 0.00000000 0.00000000 0.0000000 0.00000000 0.0000000
#> diatom 0.00000000 0.00000000 0.0000000 -0.24443109 0.0000000
#> dino 0.10617918 0.00000000 -0.1988748 -0.03007952 0.2226672
#> cyclopoid diatom dino
#> amphipod -0.1434129 0.04060264 0.0000000
#> chaetognath 0.0000000 0.00000000 0.0000000
#> cladoceran 0.0000000 0.00000000 0.0000000
#> calanoid.lg -0.1935099 0.01865910 0.0000000
#> calanoid.sm 0.0000000 -0.08207196 -0.0731972
#> cyclopoid 0.4558332 0.00000000 0.0000000
#> diatom 0.0000000 0.18078937 0.0000000
#> dino -0.2830292 0.00000000 0.1804134