opt.ssm.GRW {paleoTS} | R Documentation |
Fit evolutionary models using state-space models (SSM)
Description
Fit evolutionary models using state-space models (SSM)
Usage
opt.ssm.GRW(y, pool = TRUE, cl = list(fnscale = -1), hess = FALSE)
opt.ssm.URW(y, pool = TRUE, cl = list(fnscale = -1), hess = FALSE)
opt.ssm.Stasis(y, pool = TRUE, cl = list(fnscale = -1), hess = FALSE)
opt.ssm.StrictStasis(y, pool = TRUE, cl = list(fnscale = -1), hess = FALSE)
opt.ssm.OU(y, pool = TRUE, cl = list(fnscale = -1), hess = FALSE)
opt.ssm.ACDC(y, pool = TRUE, cl = list(fnscale = -1), hess = FALSE)
opt.ssm.covOU(y, z, pool = TRUE, cl = list(fnscale = -1), hess = FALSE)
opt.ssm.URWshift(y, gg, pool = TRUE, cl = list(fnscale = -1), hess = FALSE)
opt.ssm.covOU_vshift(
y,
z,
gg,
pool = TRUE,
cl = list(fnscale = -1),
hess = FALSE
)
Arguments
y |
a |
pool |
if |
cl |
optional control list, passed to |
hess |
if |
z |
a covariate vector, used only for the covOU models |
gg |
a grouping vector, used only for the URWshift and covOU_vshift models |
Details
These functions use a state space model formulation to compute likelihoods and fit models.
Functions to fit the OU covariate tracking models (covOU
, covOU_vshift
) require a covariate argument, z
.
At present, only the OU covariate tracking with a shift in the step variance (covOU_vshift
) requires the grouping vector argument (gg
).
Value
a paleoTSfit
object with the model fitting results
Note
For GRW, URW, Stasis, StrictStasis, ACDC and OU models, it will likely be easier to use the convenience function fitSimple
with argument method = "SSM"
.
The grouping vector, gg
, is a vector of length equal to the number of samples. It has one element for each sample and takes
integer value from 1 to the number of sample groups separated by shiftpoints. See the example below.
See Also
Examples
y <- sim.GRW(ns = 30, vs = 2)
w1 <- opt.ssm.URW(y)
gg <- rep(1:2, each = 15) # shift occurs immediately after sample 15
w2 <- opt.ssm.URWshift(y, gg = gg) # test model in which the step variance shifts
compareModels(w1, w2)