Print a species_mix model object.

Source: R/species_mix_s3-class.R

Print a species_mix model object.

# S3 method for species_mix
print(x, ...)

Arguments

x

A model object.
\dots

Ignored

Examples


#Print information about a species_mix model
# \donttest{
library(ecomix)
set.seed(42)
sam_form <- stats::as.formula(paste0('cbind(',paste(paste0('spp',1:20),
collapse = ','),")~x1+x2"))
sp_form <- ~ 1
beta <- matrix(c(-2.9,-3.6,-0.9,1,.9,1.9),3,2,byrow=TRUE)
dat <- data.frame(y=rep(1,100),x1=stats::runif(100,0,2.5),
x2=stats::rnorm(100,0,2.5))
dat[,-1] <- scale(dat[,-1])
simulated_data <- species_mix.simulate(archetype_formula = sam_form,species_formula = sp_form,
data = dat,beta=beta,family="bernoulli")

#> Random alpha from normal (-1,0.5) distribution
fm1 <- species_mix(archetype_formula = sam_form,species_formula = sp_form,
data = simulated_data, family = 'bernoulli',  nArchetypes=3)

#> SAM modelling
#> There are 3 archetypes to group the species into
#> There are 100 site observations for 20 species
#> The model for the archetype (grouping) is ~x1 + x2
#> The model for the species is ~1
#> You are implementing a bernoulli Species Archetype Model.
#> Using ECM algorithm to find starting values; using 1 refits
#> ECM restart 1 of 1
#> Initialising starting values
#> Initial groups parameter estimates by K-means clustering
#> Iteration: 1 | New loglik -950.729 | Ratio loglik 0
#> Iteration: 2 | New loglik -829.843 | Ratio loglik 0.872849
#> Iteration: 3 | New loglik -820.246 | Ratio loglik 0.988434
#> Iteration: 4 | New loglik -819.839 | Ratio loglik 0.999504
#> initial  value 819.837658 
#> iter  10 value 819.706575
#> final  value 819.703416 
#> converged
print(fm1)# }

#> bernoulli species_mix model
#> 
#> Pi
#> Archetype1 Archetype2 Archetype3 
#>       0.25       0.40       0.35 
#> 
#> Coefficients
#> $alpha
#>       spp1       spp2       spp3       spp4       spp5       spp6       spp7 
#> -0.8017227 -1.6402031 -0.5752349 -1.0844096 -1.0206816 -1.1776675 -0.7334905 
#>       spp8       spp9      spp10      spp11      spp12      spp13      spp14 
#> -1.2036925 -1.6417828 -0.1856826 -0.8567273 -1.3909615 -0.7040057 -0.7040057 
#>      spp15      spp16      spp17      spp18      spp19      spp20 
#> -0.8934080 -0.3780058 -1.3858329 -1.0552211 -1.2036925 -0.4298861 
#> 
#> $beta
#>                    x1         x2
#> Archetype1 -2.9107151 -3.5524869
#> Archetype2 -0.8299319  0.9551632
#> Archetype3  0.9916068  1.9873571
#>