Extracts estimated coefficients from a fitted multinomial state-space model.
Usage
# S3 method for class 'mnTS'
coef(object, ...)Arguments
- object
An object of class
"mnTS", as returned by themnTSfunction.- ...
Additional arguments (currently unused).
Value
A matrix of estimated coefficients. When an information matrix
is available it has columns Coef., se, t and
P; otherwise it holds point estimates only.
Examples
# A small, fast example: the reference taxon plus two others over the first
# 60 time steps. See the package vignette for a full analysis.
data(story_pollen_matrix)
data(story_char_matrix)
Y_all <- story_pollen_matrix[, 1:3]
sample_idx <- which(rowSums(Y_all) != 0)
sample_idx <- sample_idx[sample_idx <= 60]
Y <- Y_all[sample_idx, ]
X <- scale(story_char_matrix)[1:60, , drop = FALSE]
n <- ncol(Y)
# NA = estimate, a number = hold fixed at that value.
B0.fixed <- matrix(c(0, rep(NA, n - 1)), nrow = 1, ncol = n)
B.fixed <- matrix(NA, nrow = ncol(X), ncol = n)
B.fixed[, 1] <- 0 # reference taxon
V.fixed <- matrix(NA, n, n)
V.fixed[1] <- 1 # identifiability constraint
C.start <- 0.5 * diag(n) # self-regulation only
C.fixed <- C.start
C.fixed[C.fixed != 0] <- NA
# \donttest{
ts_mod <- mnTS(Y = Y, X = X, Tsample = sample_idx,
B0.fixed = B0.fixed, B.fixed = B.fixed,
C.start = C.start, C.fixed = C.fixed,
V.fixed = V.fixed, dispersion.fixed = 1)
coef(ts_mod)
#> Coef. se t
#> hardwood 0.36591181 NaN NaN
#> Fagus grandifolia 0.07421799 0.64074684 0.11583044
#> sp.other.other 0.91457579 NaN NaN
#> sp.hardwood.hardwood 0.87690755 NaN NaN
#> sp.Fagus grandifolia.Fagus grandifolia 0.95111844 0.02747347 34.61952616
#> char_acc.hardwood -0.01060566 0.11612721 -0.09132796
#> char_acc.Fagus grandifolia -0.20874064 0.15047134 -1.38724516
#> P
#> hardwood NaN
#> Fagus grandifolia 9.077869e-01
#> sp.other.other NaN
#> sp.hardwood.hardwood NaN
#> sp.Fagus grandifolia.Fagus grandifolia 1.284612e-262
#> char_acc.hardwood 9.272320e-01
#> char_acc.Fagus grandifolia 1.653670e-01
# }